T A B L E O F C O N T E N T S 1-11

Transcription

1 T A B L E O F C O N T E N T S 1-11 Chapter 1: Introduction... 1 Chapter 2: Drainage Control Activities by the Grassland Area Farmers Chapter 3: Flow and Salinity Monitoring Chapter 4: Water Quality Monitoring Chapter 5: Flow, Salt and Selenium Mass Balances in the San Luis Drain Chapter 6: Project Impacts on San Joaquin River Chapter 7: Chapter 7: Biological Effects of the Grassland Bypass Project at sites C, D, and I Biological Effects of the Grassland Bypass Project at sites E, G, H and R Chapter 8: Toxicity Testing for the Grassland Bypass Project Chapter 9: Sediment Monitoring in the San Luis Drain, Mud and Salt Sloughs Chapter 10: Sediment Quantity in the San Luis Drain Chapter 11: Quality Assurance Chapter 12: Grassland Bypass Project Peer Review

2

3 CHAPTER 1: INTRODUCTION 1 01 INTRODUCTION Michael C. S. Eacock 1 Jeffrey E. Papendick 2 1 Project Manager/Soil Scientist, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California meacock@usbr.gov 2 Natural Resources Technician, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California jpapendick@usbr.gov The Grassland Bypass Project (GBP) completed its eighteenth year of operation on December 31, The Grassland Area Farmers continued to reduce the amount of agricultural drainage water produced in the Grassland Drainage Area (GDA), preventing the discharge of this water into local Grassland wetland water supply channels, and improved the quality of water in the San Joaquin River. This report has been prepared by the multi-agency Data Collection and Review Team (DCRT) as a review and evaluation of the monitoring program that was conducted through December It builds upon prior reports to discern changes in environmental conditions since the GBP began in October BACKGROUND The GBP is based upon an agreement 3 between the U.S. Bureau of Reclamation (Reclamation) and the San Luis and Delta-Mendota Water Authority (Authority) to use a 28-mile segment of the San Luis Drain to convey agricultural subsurface drainage water from the GDA to Mud Slough (North), a tributary of the San Joaquin River. The purposes of the GBP are: 1. to continue the separation of unusable agricultural drainage water discharged from the GDA from wetland water supply conveyance channels for the period ; and, 2. to facilitate drainage management that maintains the viability of agriculture in the GDA and promotes continuous improvement in water quality in the San Joaquin River The GBP has removed agricultural drainage water from channels that supply water to more than 160,000 acres of wetlands and wildlife areas in the Grasslands Watershed. Figure 1 is a map that shows the location of the GDA and monitoring stations along tributaries of the San Joaquin River. Figure 2 is a schematic diagram of the Project with the location of monitoring sites discussed in this report. Figure 1 in Chapter 2 is a map that shows the location of the GDA in relation to the State and Federal wildlife areas. The first Use Agreement was signed November 3, 1995, and the Authority conveyed drainage water in the San Luis Drain from September 27, 1996 to September 30, The second Use Agreement, executed on September 27, 2001, allowed the Authority to use the San Luis Drain and continue the Project through December 31, The third use agreement, signed on December 22, 2009, allows the Authority to continue to use the San Luis Drain through December 31, All three Use Agreements have many conditions, including the assessment of Drainage Incentive Fees to be imposed when monthly or annual selenium or salt loads are exceeded. The fees are to be used for programs or actions that will assist in meeting selenium load values, salinity load values and discharge goals, water quality objectives in the drainage area, and/or will enhance wildlife values in the GDA or adjacent areas. 3 U.S. Bureau of Reclamation and the San Luis and Delta-Mendota Water Authority, December 22, Agreement for Continued Use of the San Luis Drain for the Period January 1, 2010 to December 31, Agreement No. 10-WC

4 2 GRASSLAND BYPASS PROJECT The 2009 Use Agreement provides Incentive Fee Credits when annual and monthly discharges are more than 10 percent below the respective load values specified in Appendix C (Selenium) and Appendix E (Salinity). Tables 3a and 4a list the monthly incentive credits that have been accrued between 2012 and 2014; Tables 3c and 4c list the annual incentive credits. Note that the Authority has accrued 18,417 selenium incentive credits and more than 839,484 salinity incentive credits over the life of the project that may be applied against future monthly or annual exceedance through December The California Regional Water Quality Control Board, Central Valley Region (Regional Board), issued Waste Discharge Requirements (WDR) 4 in 2001 to Reclamation and the Authority that specify further conditions for discharging drainage water into Mud Slough (North). The monitoring requirements for the WDR (Table 1) are the basis for the monitoring program discussed in this report. This report summarizes Project activities and accomplishments for and compares annual averages and totals for the entire seventeen years of the Project HIGHLIGHTS 2012 was dry according to the San Joaquin River Index. Annual rainfall varied from 4.54 to 6.85 inches measured at five weather stations located across the Grasslands Watershed (Table 2c). Figure 3 shows the pattern of daily rainfall and flow from the GDA during Storms in late March resulted in a peak flow of 74.7 cfs in the SLD. The Grasslands Area Farmers controlled drainage and met the annual selenium load value for 2012 (Figure 4). Monthly selenium loads discharged from the GDA were less than the Selenium Load Values specified in the 2009 Use Agreement (Table 3a and Figure 5). The annual selenium load discharged from the GDA was 690 pounds, 72 percent below the Annual Load Value of 2496 pounds (Table 3c). Monthly salt loads discharged from the GDA met the Load Values specified in the 2009 Use Agreement with one exceedance in December 2012 of 307 tons (Table 4a and Figure 6). The project discharged about 38,650 tons of salt in 2012, which was 61 percent below the Annual Salinity Load Value of 98,600 tons (Table 4c) 2013 HIGHLIGHTS 2013 was critical according to the San Joaquin River Index. Annual rainfall varied from 2.53 to 3.79 inches measured at five weather stations located across the Grasslands Watershed (Table 2c). Figure 3 shows the pattern of daily rainfall and flow from the GDA during Storms in late January resulted in a peak flow of 42.9 cfs in the SLD. The Grasslands Area Farmers controlled drainage and met the annual selenium load value for 2013 (Figure 4). Monthly selenium loads discharged from the GDA were less than the Selenium Load Values specified in the 2009 Use Agreement (Table 3a and Figure 5). The annual selenium load discharged from the GDA was 561 pounds, 48 percent below the Annual Load Value of 1075 pounds (Table 3c). Monthly salt loads discharged from the GDA met the Load Values specified in the 2009 Use Agreement eight of twelve months (Table 4a and Figure 6). Exceedances occurred in September, October, November, and December Exceedance values are in Table 4a. The project discharged about 45,830 tons of salt in 2013, which was 21 percent below the Annual Salinity Load Value of 57,999 tons (Table 4c) 2014 HIGHLIGHTS 2014 was critical according to the San Joaquin River Index. Annual rainfall varied from 3.34 to 8.32 inches measured at five weather stations located across the Grasslands Watershed (Table 2c). Figure 3 shows the pattern of daily rainfall and flow from the GDA during Storms during the end of the year resulted in a peak flow of 97.6 cfs in the SLD. The Grasslands Area Farmers controlled drainage and met the annual selenium load value for 2014 (Figure 4). 4 California Regional Water Quality Control Board, Central Valley Region, September 21, Waste Discharge Requirements No for the San Luis & Delta-Mendota Water Authority and the United States Department of the Interior, Grassland Bypass Channel Project (Phase II), Fresno and Merced Counties.

5 CHAPTER 1: INTRODUCTION 3 In December 2014, there was an exceedance of the Selenium Load Value specified in the 2009 Use Agreement (Table 3a and Figure 5). 173 pounds of selenium was discharged in December 2014 with a Load Value of 152 pounds. The annual selenium load discharged from the GDA was 461 pounds, 57 percent below the Annual Load Value of 1075 pounds (Table 3c). Monthly salt loads discharged from the GDA met the Load Values specified in the 2009 Use Agreement eight of twelve months (Table 4a and Figure 6). Exceedances occurred in January, February, November, and December Exceedance values are listed in Table 4a. The project discharged about 42,820 tons of salt in 2014, which was 26 percent below the Annual Salinity Load Value of 57,999 tons (Table 4c) CURRENT LOADS AND CONCENTRATIONS COMPARED TO PRE-PROJECT CONDITIONS Table 5 presents the concentrations and loads of selenium, boron, and salt in water discharged from the GDA for Water Years through Note that the volume of drain water and loads discharged from the GDA during WY 2012 through WY 2014 were much less than the pre-project years: Summary of Table 5 GRASSLANDS DRAINAGE AREA WY Pre-Project Average VOLUME (ACRE-FEET) SELENIUM (POUNDS) BORON (TONS) SALTS (TONS) 49,760 8, ,510 WY , ,240 WY , ,270 WY , ,160 Table 6 lists the annual loads of selenium, boron, and salt discharged from the Grasslands watershed (Mud and Salt Sloughs) for Water Years 1986 through The volume of water in the streams has increased since 1993, mainly due to larger deliveries of CVP water to local refuges under federal law 6. Note that the volume of water and loads discharged from the Grasslands watershed during WY 2012 through WY 2014 were much less than the pre-project years: Summary of Table 6 GRASSLANDS WATERSHED (MUD & SLAT SLOUGHS) WY Pre-Project Average VOLUME (ACRE-FEET) SELENIUM (POUNDS) BORON (TONS) 202,320 7, ,290 SALTS (TONS) WY , ,290 WY , ,650 WY , ,870 5 Water Year = October 1 September 30 6 Title XXXIV, Central Valley Project Improvement Act, Reclamation Projects Authorization and Adjustments Act of 1992 (Public Law Oct. 30, 1992)

6 4 GRASSLAND BYPASS PROJECT Table 7 lists the annual loads of selenium, boron, and salt in the San Joaquin River below the Merced River for Water Years 1986 through Note that loads in the river during WY 2012 through WY 2014 were much less than the pre-project years: Summary of Table 7 SAN JOAQUIN RIVER BELOW MER- CED RIVER (PATTERSON OR CROWS LANDING) VOLUME (ACRE-FEET) SELENIUM (POUNDS) BORON (TONS) SALTS (TONS) WY Pre-Project Average 1,066,320 8, ,950 WY ,220 1, ,280 WY , ,380 WY , ,480 ADDITIONAL REPORTS AND STUDIES Delta-Mendota Canal Water Quality Monitoring Reclamation continued to measure selenium and salinity in water in the Delta-Mendota Canal and Mendota Pool. These facilities convey water to the farms and wetlands in the Grasslands Basin. Daily composite samples are collected from four sites to study the temporal and local changes in water quality due to the operation of the canal, drainage sumps, and tail water inlet structures. These data are published in monthly reports and are available upon request from Reclamation. San Joaquin River Restoration Program (SJRRP) In 1988, a coalition of environmental groups, led by the Natural Resources Defense Council (NRDC), filed a lawsuit challenging the renewal of long-term water service contracts between the United States and the Central Valley Project Friant Division contractors. After more than 18 years of litigation of this lawsuit, known as NRDC et al. v. Kirk Rodgers et al., a Stipulation of Settlement (Settlement) was reached. On September 13, 2006, the Settling Parties, including NRDC, Friant Water Users Authority, and the U.S. Departments of the Interior and Commerce, agreed on the terms and conditions of the Settlement, which was subsequently approved by the U.S. Eastern District Court of California on October 23, The SJRRP is a comprehensive long-term effort to restore flows in the San Joaquin River from Friant Dam to the confluence of the Merced River, ensure irrigation supplies to Friant water users, and restore a self-sustaining fishery in the river. The SJRRP has two primary goals: Restoration Goal To restore and maintain fish populations in good condition in the main stem San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally reproducing and self-sustaining populations of salmon and other fish. Water Management Goal To reduce or avoid adverse water supply impacts on all of the Friant Division long-term contractors that may result from the Interim Flows and Restoration Flows provided for in the Settlement. Reclamation and other agencies are conducting environmental monitoring along the river between Friant Dam and the confluence with the Merced River at Hills Ferry. The two-mile portion of the river between Mud Slough and Hills Ferry conveys water from the GBP. GBP data are being used for baseline studies and future monitoring will be coordinated by both programs. No water associated with the SJRRP flowed past Hills Ferry during WY 2012, WY 2013 and WY 2014.

7 CHAPTER 1: INTRODUCTION 5 Water Quality Monitoring in the San Joaquin River at Hills Ferry (H) The Grassland Area Farmers collected water samples from the San Joaquin River above the Merced River at Hills Ferry (Station H) each week up to October 2013 (Table 8). At the end of October 2013, USBR took over sampling and moved the sampling location to the San Joaquin River at Chine Island (Station R). This location provided easier site access and is more representative of the impacts of the Mud Slough discharge into the San Joaquin River upstream of the confluence of the Merced River. The Station is location in the China Island State Wildlife Refuge and is approximately 1.3 miles downstream of the Mud Slough discharge. The concentration of selenium in weekly grab samples of water collected at these Stations ranged from 0.6 μg/l to 2.7 μg/l in 2012, from 0.4 μg/l to 3.5 μg/l in 2013, and from 0.4 μg/l to 3.2 μg/l in The average monthly concentration of boron ranged from 0.5 mg/l to 1.5 mg/l in 2012, from 1.1 mg/l to 2.1 mg/l in 2013, and from 0.5 mg/l to 2.4 mg/l in PROJECT ORGANIZATION The GBP involves the coordination and cooperation of the US Bureau of Reclamation (Reclamation), US Fish and Wildlife Service (USFWS), the US Geological Survey (USGS), the US Environmental Protection Agency (USEPA), the California Regional Water Quality Control Board - Central Valley Region (Regional Board), California Department of Fish and Game (CDFG), and the San Luis and Delta-Mendota Water Authority (Authority). Oversight Committee The Oversight Committee reviews progress and operation of the project including drainage reduction goals, progress in achieving water quality objectives, monitoring data, etc. It makes recommendations to the Draining Parties, Reclamation, and/or the Regional Board, as appropriate, regarding all aspects of the project, including modifications to project operation, appropriate mitigation, and termination of the Agreement if necessary. It carries out other functions required of it under this Agreement, which include determining the occurrence and extent of load exceedances, the Drainage Incentive Fees that are payable and actions or projects to be funded with Drainage Incentive Fees. The Oversight Committee is comprised of senior level representatives from Reclamation, USEPA, USFWS, CDFG, and the Regional Board. Its role is to review process and assure performance of all operations of the Project as specified in the 2009 Use Agreement, including monitoring data, compliance with selenium load reduction goals, and other relevant information. The Oversight Committee did not meet in 2012, 2013, or Technical and Policy Review Team (TPRT) The Oversight Committee appointed the TPRT to evaluate technical and policy issues. The TPRT consists of representatives of the Reclamation, USEPA, USGS, USFWS, CDFG, and the Regional Board. The TPRT is responsible for obtaining and providing the necessary information, options, and recommendations to the Oversight Committee for issues and decisions regarding the project. The TPRT did not meet during 2012, 2013, or Data Collection and Reporting Team (DCRT) The DCRT is made up of representatives of agencies that collect the monitoring data: Reclamation, USEPA, USFWS, USGS, CDFG, the Regional Board, and the Authority. The Team reviewed monthly and quarterly data reports. The DCRT completed the report. The DCRT met in August 2012 to tour samples sites in the GBP area and discuss changes to the 2013 monitoring plan. Data Management Each agency collecting data is responsible for its own internal data quality and data management procedures. Each agency submits its data to the San Francisco Estuary Institute for compilation of data and information from all sampling sites in a timely manner.

8 6 GRASSLAND BYPASS PROJECT Reporting The San Francisco Estuary Institute publishes monthly, quarterly and annual reports of data from the 14 monitoring stations depicted on Figure 2. The monthly reports present daily and weekly water quality data, including the calculated selenium load discharged at Site B, the terminus of the San Luis Drain. Quarterly data reports consist of all available data from all stations during a 3-month period. All of the GBP data reports are available at the Institute s Website: Annual reports are available on the SFEI website. Many other GBP documents are posted on the website of the Bureau of Reclamation, Mid-Pacific Region: REFERENCES Data Reports: San Francisco Estuary Institute. October 1996-December Grassland Bypass Project Monthly Reports (182 reports). Oakland, CA. San Francisco Estuary Institute. Oct Nov Dec 1996 to Oct Nov Dec Grassland Bypass Project Quarterly Data Report. (57 reports). Oakland, CA. Annual Reports: U.S Bureau of Reclamation, et al., May 12, Grassland Bypass Project Annual Report. October 1, 1996 September 30, Prepared for the Grassland Bypass Project Oversight Committee. Sacramento, California. San Francisco Estuary Institute. June Grassland Bypass Project Annual Report October 1, 1997 through September 30, Richmond, CA. (2 MB) San Francisco Estuary Institute. May Grassland Bypass Project Annual Report Richmond, CA. (7 MB) San Francisco Estuary Institute. May Grassland Bypass Project Annual Report Richmond, CA. (4 MB) San Francisco Estuary Institute. May Grassland Bypass Project Annual Report Richmond, CA. (11 MB) San Francisco Estuary Institute. July Grassland Bypass Project Report October 2001 December Richmond, CA. (15 MB) San Francisco Estuary Institute. August Grassland Bypass Project Annual Report Richmond, CA. (10 MB) sites/default/files/gbpannualreport2003.pdf San Francisco Estuary Institute, May Grassland Bypass Project Annual Report Richmond, CA. (11 MB) org/sites/default/files/gbp%20annual%20report%200405_1.pdf San Francisco Estuary Institute, July Grassland Bypass Project Annual Report Richmond, CA. (15 MB) San Francisco Estuary Institute, October Grassland Bypass Project Annual Report Richmond, CA. San Francisco Estuary Institute, October Grassland Bypass Project Annual Report Richmond, CA. In Press.

9 CHAPTER 1: INTRODUCTION 7 Phase I Documents: U.S. Bureau of Reclamation. November Finding of No Significant Impact and Supplemental Environmental Assessment. Grassland Bypass Channel Project. Interim Use of a Portion of the San Luis Drain for Conveyance of Drainage Water through Grassland Water District and Adjacent Grassland Areas. Sacramento, CA. U.S. Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority. November Agreement for Use of the San Luis Drain. Agreement No W1319. Sacramento, CA. U.S. Bureau of Reclamation et al. September Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project. Sacramento, CA. Phase II Documents: U.S. Bureau of Reclamation, Mid-Pacific Region. February Biological Assessment for the Grassland Bypass Project. Sacramento, CA. URS. May 25, Grassland Bypass Project Environmental Impact Statement and Environmental Impact Report. Oakland, CA. U. S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office. September 27, Final Biological Opinion for the Grassland Bypass Project. File Number F Sacramento, CA. U.S. Bureau of Reclamation. September 28, Record of Decision for the Grassland Bypass Project EIS/EIR. Sacramento, CA. California Regional Water Quality Control Board, Central Valley Region. September 7, Waste Discharge Requirements Order No Sacramento, CA. U.S. Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority. September 28, Agreement for Use of the San Luis Drain for the Period October 1, 2001 through December 31, Agreement No. 01-WC U.S. Bureau of Reclamation, et al. June Monitoring Program for the Operation of the Grassland Bypass Project. Prepared by the Grassland Bypass Project Data Collection and Review Team. U.S. Bureau of Reclamation, et al. August 22, Quality Assurance Project Plan for the Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project. California Regional Water Quality Control Board, Central Valley Region. May Revised Monitoring and Reporting Program for Waste Discharge Requirements Order No Sacramento, CA. Grassland Bypass Project Technical and Policy Review Team, March 2, Determination of Drainage Incentive Fees for the Winter 2005 Floods. Phase III Documents: U. S. Bureau of Reclamation, September 29, Final Environmental Impact Statement Impact Report, Continuation of the Grassland Bypass Project, Sacramento, CA. U. S. Fish and Wildlife Service, Sacramento Fish and Wildlife Office. December 18, Endangered Species Consultation on the Proposed Continuation of the Grassland Bypass Project. Sacramento, CA. U.S. Bureau of Reclamation. December 21, Record of Decision, Grassland Bypass Project, Sacramento, CA. U.S. Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority. December 22, Agreement for Continued Use of the San Luis Drain for the Period January 1, 2010 through December 31, Agreement No. 10-WC U. S. Bureau of Reclamation. May 23, Grassland Bypass Project 2011 Interim Water Quality Monitoring Program.

10 8 GRASSLAND BYPASS PROJECT Tables Table 1 Grassland Bypass Project - Monitoring Stations, Parameters, and Sampling Frequencies Table 2. Monthly Rainfall on the Grasslands Watershed Table 3a,b,c. Monthly Loads of Selenium Discharged from the San Luis Drain (Station B2) into Mud Slough Compared to Load Values Table 4a,b,c. Monthly Loads of Salt Discharged from the Grassland Drainage Area Compared to Salinity Load Values Table 5. Grassland Drainage Area - Water Years Table 6. Grassland Watershed (Mud and Salt Sloughs) - Water Years Table 7. San Joaquin River at Patterson and Crows Landing - Water Years Table 8a,b. Water Quality in the San Joaquin River at Hills Ferry (Station H) and San Joaquin River at China Island (Station R) Figures Figure 1. Map of the Grassland Bypass Project Figure 2. Grassland Bypass Project - Schematic Diagram Showing Locations of GBP Monitoring Sites Relative to Major Hydrologic Features of the Study Area Figure 3. Comparison of Rainfall and Flow from the Grassland Drainage Area Figure 4. Annual Loads of Selenium Discharged from the Grassland Drainage Area Figure 5. Selenium Discharged from the Grasslands Drainage Area Figure 6. Salts Discharged from the Grasslands Drainage Area

11 CHAPTER 1: INTRODUCTION 9 TABLE 1. GRASSLAND BYPASS PROJECT - MONITORING STATIONS, PARAMETERS, AND SAMPLING FREQUENCIES STATION / SITE / LOCATION FLOW PH ELECTRICAL CONDUCTIV- ITY TEMPERATURE BORON MOLYB- DENUM NUTRI- ENTS SELE- NIUM TOTA SUS- PENDED SOLIDS TUR- BIDITY CHRONIC AND ACUTE TOX- ICITY SEDIMENT QUALITY SEDIMENT QUANTITY BIOTA San Luis Drain A Grassland Bypass Channel Da Da Da Wg Dc Wg A A checks A A checks A A checks A A checks 1-2 A A B Water quality monitoring site Wg Wg Wg 24c, Wg Mg Mg(1) 24c Wg(2) M, Q A A B2 Terminus at Mud Slough Da 24c Da Mud Slough (north) C upstream of SLD discharge estimate Wg Wg Wg Wg Mg Mg(1) Wg M, Q Q Q D downstream of SLD discharge C, Da Wg Da, Wg Da, Wg Wg Mg Mg(1) Wg M, Q Q Q E Hwy 140 bridge Q Q I2 backwater Wg (3) Wg (3) Wg (3) Wg (3) Wg (3) Q Q Salt Slough F Hwy 165 bridge C Wg C C Wg Wg Q Q Grasslands Wetland Water Supply Channels J Camp 13 Ditch (3) Da (3) Wg Wg Wg K Agatha Canal (4) Da (3) Wg Wg Wg San Joaquin River G Fremont Ford C, Da Wg Da, Wg Da, Wg Wg Mg Mg(1) Wg Q H Hills Ferry (CDFG fish screen) Wg Wg Wg Q N Crows Landing C, Da Wg C, Dc, Wg C, Wg Dc, Wg Mg Mg(1) Dc, Wg R China Island Wg Wg Wg Wg Mg Mg(1) Wg Sampling Frequency A = Annual Da = Daily average Dc = Daily composite Mg = Monthly grab Wc = Weekly composite C = Continuous 24c = 24 hour composite M = Monthly Q = Quarterly Wg = Weekly grab Letters in Bold indicate a monitoring requirement within Waste Discharge Requirement (1) Weekly sampling: March through August, and Monthly sampling: September through February (2) Daily sampling during storm events. (3) Sampled when water is flowing past this site. (4) Discontinued monitoring for GBP in 2013.

12 10 GRASSLAND BYPASS PROJECT TABLE 2a. MONTHLY RAINFALL ON THE GRASSLANDS WATERSHED FLOW PASSING STATION A FIREBAUGH TELLES LOS BANOS PANOCHE PANOCHE LOS BANOS Water Year Average cfs Total acre-feet CIMIS 007 (1) inches CIMIS 056 (1) inches CIMIS 124 (1) inches WD (2) inches NOAA (3) inches Jan Feb Mar , Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb , Mar Apr May Jun Jul Aug Sep Oct Nov Dec , Data sources: 1. CIMIS - California Department of Water Resources, California Irrigation Management Information System 2. Panoche Water District 3. NOAA, Western Regional Climate Center, revised 24 Sep

13 CHAPTER 1: INTRODUCTION 11 TABLE 2b. ANNUAL RAINFALL ON THE GRASSLANDS WATERSHED - WATER YEARS FLOW PASSING STATION A FIREBAUGH TELLES LOS BANOS PANOCHE PANOCHE LOS BANOS Water Year Average cfs Total acre-feet CIMIS 007 (1) inches CIMIS 056 (1) inches CIMIS 124 (1) inches WD (2) inches NWS (3) inches WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , WY , TABLE 2c. ANNUAL RAINFALL ON THE GRASSLANDS WATERSHED - CALENDAR YEARS FLOW PASSING STATION A FIREBAUGH TELLES LOS BANOS PANOCHE PANOCHE LOS BANOS Calendar Year Average cfs Total acre-feet CIMIS 007 (1) inches CIMIS 056 (1) inches CIMIS 124 (1) inches WD (2) inches NWS (3) inches , , , , , , , , , , , , , , , , , ,

14 12 GRASSLAND BYPASS PROJECT TABLE 3a. MONTHLY LOADS OF SELENIUM DISCHARGED FROM THE SAN LUIS DRAIN (STATION B2) INTO MUD SLOUGH COMPARED TO LOAD VALUES MONTHLY SELENIUM LOAD VALUE (1) MONTHLY SELENIUM DISCHARGE (2) EXCEEDANCE OF MONTHLY LOAD VALUE PERCENT OF MONTHLY LOAD VALUE INCENTIVE CREDIT Jan % 259 Feb % 128 Mar % 64 Apr % 149 May % 128 Jun % 49 Jul % 63 Aug % 97 Sep % 217 Oct % 221 Nov % 198 Dec % 233 Jan % 52 Feb % 10 Mar % 29 Apr % 32 May % 39 Jun % 25 Jul % 34 Aug % 41 Sep % 44 Oct % 39 Nov % 42 Dec % 125 Jan % 112 Feb % 0 Mar % 29 Apr % 82 May % 88 Jun % 44 Jul % 59 Aug % 74 Sep % 56 Oct % 53 Nov % 33 Dec % ,646 1,712 2,950 Project Totals 82,159 60,621 18,417 Notes: (1) 2009 Use Agreement, Appendix C (2) Actual Selenium Discharge: San Francisco Estuary Institute

15 CHAPTER 1: INTRODUCTION 13 TABLE 3b. ANNUAL LOADS OF SELENIUM DISCHARGED FROM THE SAN LUIS DRAIN (STATION B/B2) INTO MUD SLOUGH COMPARED TO LOAD VALUES - WATER YEARS WATER YEAR ANNUAL SELENIUM LOAD VALUE POUNDS ANNUAL SELENIUM DISCHARGE POUNDS ANNUAL DIFFERENCE POUNDS PERCENT WY ,524 WY ,959 WY ,097 WY ,718 WY ,393 WY ,858 WY ,083 WY ,856 WY ,468 WY ,875 WY ,034 WY ,096 6, % WY ,096 8,774 1,678 24% WY ,813 5,129-1,684-25% WY ,528 4,597-1,931-30% WY ,246 4,377-1,869-30% WY ,360 3,941-1,419-26% WY ,027 4,025-1,002-20% WY ,696 3, % WY ,585 4, % WY ,148 3, % WY ,625 2,552-1,073-30% WY ,301 1,735-1,566-47% WY ,169 1,252-1,917-60% WY ,093 1,577-2,516-61% WY ,531 2,055-2,476-55% WY , ,837-71% WY , % WY , % TABLE 3c. ANNUAL LOADS OF SELENIUM DISCHARGED FROM THE SAN LUIS DRAIN (STATION B/B2) INTO MUD SLOUGH COMPARED TO LOAD VALUES - CALENDAR YEARS CALENDAR YEAR ANNUAL SELENIUM LOAD VALUE POUNDS ANNUAL SELENIUM DISCHARGE POUNDS ANNUAL DIFFERENCE POUNDS PERCENT ,096 6, % ,096 8,883 1,787 25% ,813 4,990-1,823-27% ,528 4,506-2,022-31% ,144 4,300-1,844-30% ,327 4,174-1,153-22% ,995 4, % ,664 3, % ,566 4, % ,480 3, % ,545 2,274-1,271-36% ,236 1,686-1,550-48% ,296 1,249-2,047-62% ,162 1,539-2,623-63% ,480 1,997-2,483-55% , ,806-72% , % , %

16 14 GRASSLAND BYPASS PROJECT TABLE 4a. MONTHLY LOADS OF SALT DISCHARGED FROM THE GRASSLAND DRAINAGE AREA COMPARED TO SALINITY LOAD VALUES MONTHLY SALINITY LOAD VALUES (1) ACTUAL MONTHLY DISCHARGE (2) EXCEEDANCE OF MONTHLY LOAD VALUE PERCENT OF MONTHLY LOAD VALUE INCENTIVE CREDIT TONS TONS TONS PERCENT TONS Jan ,282 2,940 40% 4,342 Feb ,524 2,910 25% 8,614 Mar ,653 6,120 45% 7,533 Apr ,047 3,930 39% 6,117 May ,847 3,340 34% 6,507 Jun ,185 3,600 35% 6,585 Jul ,293 4,530 44% 5,763 Aug ,134 2,690 29% 6,444 Sep ,825 1,090 23% 3,735 Oct ,706 1,150 31% 2,556 Nov ,851 1,790 46% 2,061 Dec ,253 4, % 0 Jan ,283 4,130 96% 0 Feb ,779 4,030 59% 2,749 Mar ,031 4,160 52% 3,871 Apr ,910 4,320 73% 1,590 May ,792 3,360 58% 2,432 Jun ,991 3,040 51% 2,951 Jul ,055 5,270 87% 785 Aug ,373 5,230 97% 0 Sep ,838 3, % 0 Oct ,180 3,440 1, % 0 Nov ,265 2, % 0 Dec ,502 2, % 0 Jan ,283 4, % 0 Feb ,779 6, % 0 Mar ,031 3,990 50% 4,041 Apr ,910 2,730 46% 3,180 May ,792 1,670 29% 4,122 Jun ,991 2,980 50% 3,011 Jul ,055 1,960 32% 4,095 Aug , % 5,253 Sep , % 2,758 Oct , % 2,110 Nov ,265 3,620 1, % 0 Dec ,502 14,030 11, % , , ,205 Project totals 1,885,141 1,040, ,484 Notes: (1) Appendix E of the 2009 Use Agreement (2) Monthly Loads calculated from flow and salinity data reported by the San Luis and Delta-Mendota Water Authority for Station A.

17 CHAPTER 1: INTRODUCTION 15 TABLE 4b. ANNUAL LOADS OF SALT DISCHARGED FROM THE SAN LUIS DRAIN (STATION B/B2)INTO MUD SLOUGH COMPARED TO LOAD VALUES - WATER YEARS CALENDAR YEAR ANNUAL SALINITY LOAD VALUE TONS ANNUAL SALINITY DIS- CHARGE TONS ANNUAL DIFFERENCE TONS PERCENT WY ,250 WY ,526 WY ,301 WY ,420 WY ,265 WY ,899 WY ,327 WY ,021 WY ,495 WY ,530 WY ,526 WY ,750 WY ,340 WY ,910 WY ,250 WY ,080 WY , ,220-79,080-42% WY , ,600-68,290-38% WY , ,700-61,676-36% WY , ,990-41,255-25% WY , ,070-56,776-34% WY ,977 78,470-77,507-50% WY ,464 55,310-93,154-63% WY ,350 47,880-86,470-64% WY ,752 59, ,462-64% WY ,240 86,430-80,810-48% WY ,893 43,240-63,653-60% WY ,862 44,270-18,592-30% WY ,999 34,160-23,839-41% TABLE 4C. ANNUAL LOADS OF SALT DISCHARGED FROM THE SAN LUIS DRAIN (STATION B/B2) INTO MUD SLOUGH COMPARED TO LOAD VALUES - CALENDAR YEARS CALENDAR YEAR ANNUAL SALINITY LOAD VALUE TONS ANNUAL SALINITY DIS- CHARGE TONS ANNUAL DIFFERENCE TONS PERCENT , , , , , , ,040-75,260-40% , ,260-66,525-37% , ,900-59,371-35% , ,650-44,196-26% , ,220-54,626-33% , , ,559-58% ,841 48,210-85,631-64% ,941 58, ,711-65% ,883 88,440-79,443-47% ,847 83,580-84,267-50% ,600 38,650-59,950-61% ,999 45,830-12,169-21% ,999 42,820-15,179-26%

18 16 GRASSLAND BYPASS PROJECT TABLE 5. GRASSLAND DRAINAGE AREA - WATER YEARS FLOW WEIGHTED LOADS FLOW WEIGHTED CONCENTRATION WATER YEAR (1) FLOW ACRE-FEET SELENIUM POUNDS BORON TONS TDS TONS SELENIUM ΜG/L BORON MG/L EC ΜS/CM TDS MG/L REFERENCE WY ,006 9, , ,351 (2) WY ,902 10, , ,371 (2) WY ,327 10, , ,660 (2) WY ,186 8, , ,747 (2) WY ,662 7, , ,023 (2) WY ,290 5, , ,261 (2) WY ,533 5, , ,307 (2) WY ,197 8, , ,267 (2) WY ,670 8, , ,261 (2) WY ,574 11, , ,034 (2) WY ,978 10, , ,742 (3) Pre-Project Averages 49,760 8, , ,910 WY ,800 6, , ,480 3,315 (4) WY ,574 8, , ,838 3,580 (4) WY ,510 5, , ,820 3,567 (4) WY ,330 4, , ,614 3,414 (4) WY ,050 4, , ,605 3,408 (4) WY ,816 3, , ,397 3,254 (4) WY ,246 4, , ,552 3,368 (4) WY ,372 3, , ,445 3,290 (4) WY ,540 4, , ,584 3,392 (4) WY ,080 3, , ,782 3,538 (4) WY ,777 2, , ,660 3,449 (4) WY ,220 1, , ,151 3,072 (4) WY ,340 1, , ,827 2,832 (4) WY ,610 1, , ,335 3,208 (4) WY ,540 2, , ,211 3,856 (4) WY , , ,006 3,704 (4) WY , , ,392 3,990 (4) WY2014 4, , ,245 5,361 (4) Project Averages 21,630 3, , ,775 3, Water Year: October - September References: 2. CVRWQCB, February Loads of Salt, Boron, and Selenium in the Grassland Watershed and Lower San Joaquin River, October 1985 to September 1995; Volume I: Load Calculations. Table CVRWQCB, December Agricultural Drainage Contribution to Water Quality in the Grassland Watershed of Western Merced County, California: October September 1997 (Water Years 1996 and 1997). Table Flow, salt concentrations and loads calculated from data for GBP Site A; selenium loads and concentrations calculated for GBP Site B2.

19 CHAPTER 1: INTRODUCTION 17 TABLE 6. GRASSLAND WATERSHED (MUD AND SALT SLOUGHS) - WATER YEARS FLOW WEIGHTED LOADS FLOW WEIGHTED CONCENTRATION WATER YEAR (1) FLOW ACRE-FEET SELENIUM POUNDS BORON TONS TDS TONS SELENIUM ΜG/L BORON MG/L EC ΜS/CM TDS MG/L REFERENCE WY ,316 6, , ,279 (2) WY ,843 7, , ,380 (2) WY ,454 8, , ,455 (2) WY ,393 8, , ,354 (2) WY ,656 7, , ,438 (2) WY ,162 3, , ,595 (2) WY ,428 2, , ,699 (2) WY ,955 6, , ,473 (2) WY ,546 7, , ,520 (2) WY ,769 10, , ,392 (2) WY ,948 9, , ,311 (3) Pre-Project averages 202,320 7, , ,450 WY ,930 7, , ,859 1,277 (4) WY ,670 8,648 1, , ,972 1,350 (4) WY ,130 5, , ,748 1,198 (4) WY ,490 3, , ,788 1,223 (4) WY ,750 4, , ,912 1,311 (4) WY ,160 3, , ,015 1,381 (4) WY ,140 4,020 1, , ,887 1,294 (4) WY ,520 3, , ,879 1,290 (4) WY ,880 4, , ,794 1,230 (4) WY ,900 3, , ,631 1,120 (4) WY ,500 2, , ,771 1,216 (4) WY ,560 1, , ,968 1,350 (4) WY ,410 1, , ,096 1,438 (4) WY ,250 2, , ,874 1,285 (4) WY ,000 2, , ,631 1,116 (4) WY , , ,749 1,201 (4) WY , , ,872 1,280 (4) WY , , ,647 1,819 (4) Project Averages 208,740 3, , ,894 1, Water Year - October - September References: 2. CVRWQCB, February Loads of Salt, Boron, and Selenium in the Grassland Watershed and Lower San Joaquin River, October 1985 to September 1995; Volume I: Load Calculations. Table CVRWQCB, December Agricultural Drainage Contribution to Water Quality in the Grassland Watershed of Western Merced County, California: October September 1997 (Water Years 1996 and 1997) Table Loads and concentrations calculated from data for GBP Sites D and F

20 18 GRASSLAND BYPASS PROJECT TABLE 7. SAN JOAQUIN RIVER AT PATTERSON AND CROWS LANDING - WATER YEARS WATER YEAR (1) FLOW ACRE-FEET FLOW WEIGHTED LOADS SELENIUM POUNDS BORON TONS TDS TONS FLOW WEIGHTED CONCENTRATION SELENIUM ΜG/L BORON MG/L EC ΜS/CM TDS MG/L REFERENCE WY ,676,764 10,568 1, , (2) WY ,135 8, , (2) WY ,412 9, , (2) WY ,398 7, , (2) WY ,163 6, , (2) WY ,223 3, , ,059 (2) WY ,151 3, , (2) WY ,230 8, , (2) WY ,301 7, , (2) WY ,504,034 14,291 1,148 1,236, (2) WY ,445,730 10, , (3) Pre-Project Averages 1,066,320 8, , WY ,452,870 12,329 3,012 1,080, (4) WY ,904,910 15,821 2,814 1,511, (4) WY ,015,480 6, , (4) WY ,027,440 6, , (4) WY ,430 5, , , (4) WY ,960 4, , , (4) WY ,130 4, , , (4) WY ,550 4, , , (4) WY ,721,000 5,297 1, , (4) WY ,437,650 5,652 1, , (4) WY ,180 2, , , (4) WY ,500 2, , (4) WY ,670 1, , , (4) WY ,070 2, , (4) WY ,190,910 3,823 1, , (4) WY ,220 1, , , (4) WY , , , (4) WY , , , (4) Project Averages 1,354,610 4,729 1, , Water Year - October - September References: 2. CVRWQCB, February Loads of Salt, Boron, and Selenium in the Grassland Watershed and Lower San Joaquin River, October 1985 to September 1995; Volume I: Load Calculations. Table CVRWQCB, December Water Quality of the Lower San Joaquin River: Lander Avenue to Vernalis, October September 1997 (Water Years 1996 and 1997) Table Concentrations and loads calculated from data for GBP Site N

21 CHAPTER 1: INTRODUCTION 19 TABLE 8a. WATER QUALITY IN THE SAN JOAQUIN RIVER ABOVE MERCED RIVER CONFLUENCE (STATIONS H AND R) FLOW ACRE-FEET SPECIFIC CONDUCTANCE ΜMHOS/CM SELENIUM ΜG/L BORON MG/L Jan ,430 1, Feb ,480 2, Mar ,320 2, Apr ,250 2, May ,110 2, Jun ,930 1, Jul ,400 1, Aug ,870 1, Sep ,330 1, Oct ,400 1, Nov ,470 1, Dec ,260 1, Jan ,900 1, Feb ,550 2, Mar ,060 2, Apr ,940 2, May ,290 1, Jun ,260 1, Jul ,180 1, Aug ,290 1, Sep ,250 1, Oct ,180 1, Nov ,840 1, Dec ,970 2, Jan ,940 2, Feb ,102 2, NA Mar ,575 2, Apr ,055 2, May ,066 3, Jun ,134 3, Jul , Aug , Sep , Oct ,592 2, Nov ,309 2, Dec ,700 1, Data Source: USGS (H) USGS (H) USBR (R)* USBR (R)* * Se and B data collected by SLDMWA at site H until October 2013 TABLE 8b. SUMMARY STATISTICS, OCTOBER DECEMBER 2014 FLOW ACRE-FEET SPECIFIC CONDUCTANCE ΜMHOS/CM SELENIUM ΜG/L BORON MG/L Maximum 150,290 3, Minimum < Median 18,415 1, Average 32,396 1, Standard deviation 38, Number of Samples

22 20 GRASSLAND BYPASS PROJECT FIGURE 1 MAP OF THE GRASSLAND BYPASS PROJECT

23 CHAPTER 1: INTRODUCTION 21 FIGURE 2. GRASSLAND BYPASS PROJECT - SCHEMATIC DIAGRAM SHOWING LOCATIONS OF GBP MONITORING SITES RELATIVE TO MAJOR HYDROLOGIC FEATURES OF THE STUDY AREA

24 22 GRASSLAND BYPASS PROJECT FIGURE 3. COMPARISON OF RAINFALL AND FLOW FROM THE GRASSLAND DRAINAGE AREA

25 FIGURE 4. GRASSLAND BYPASS PROJECT ANNUAL LOADS OF SELENIUM DISCHARGED FROM THE GRASSLAND DRAINAGE AREA CHAPTER 1: INTRODUCTION 23

26 24 GRASSLAND BYPASS PROJECT FIGURE 5a. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2012 FIGURE 5b. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2013 FIGURE 5c. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2014

27 CHAPTER 1: INTRODUCTION 25 FIGURE 6a. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2012 FIGURE 6b. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2013 FIGURE 6c. SELENIUM DISCHARGED FROM THE GRASSLANDS DRAINAGE AREA-2014

28 26 GRASSLAND BYPASS PROJECT

29 02 DRAINAGE CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 27 CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS Joseph C. McGahan 1 1 Drainage Coordinator INTRODUCTION The Grassland Area Farmers formed a regional drainage entity in March 1996 under the umbrella of the San Luis and Delta-Mendota Water Authority to implement the Grassland Bypass Project. The Project consolidates subsurface drainage flows on a regional basis and utilizes a portion of the Federal San Luis Drain to convey the flows around the habitat areas (see Figure 1). Participants include the Charleston Drainage District, Firebaugh Canal Water District, Pacheco Water District, Panoche Drainage District and the Camp 13 Drainage District (located in part of Central California Irrigation District). Broadview Water District and Widren Water District were original members but have withdrawn. This entity includes approximately 97,000 gross acres of irrigated farmland on the westside of the San Joaquin Valley, referred to as the Grassland Drainage Area. The area is highly productive, producing an estimated $400 Million annually in agricultural crop market value, with an additional estimated $250 Million generated for the local and regional economies, for a total estimated economic value of over $600 Million. The Grassland Area Farmers have implemented several activities aimed at reducing discharge of subsurface drainage waters to the San Joaquin River. These activities have included the Grassland Bypass Project and the San Joaquin River Improvement Project (SJRIP). They also include: formation of a regional drainage entity, newsletters and other communication with the farmers, a monitoring program, using State Revolving Fund loans for improved irrigation systems, utilizing and installing drainage recycling systems to mix subsurface drainage water with irrigation supplies under strict limits, tiered water pricing and a tradable loads programs. GRASSLAND BYPASS PROJECT The Grassland Bypass Project is an innovative program that was designed to improve water quality in the channels used to deliver water to wetland areas. Prior to the Project, subsurface drainage water was conveyed through those channels enroute to the San Joaquin River which limited their availability to deliver high-quality habitat supplies. The Project consolidates subsurface drainage flows on a regional basis and utilizes a portion of the federal San Luis Drain to convey the flows around the habitat areas. Negotiations between the San Luis & Delta-Mendota Water Authority and the U S Bureau of Reclamation to utilize a portion of the San Luis Drain for the Project commenced in Stakeholders included in the process were: U.S. Environmental Protection Agency, U.S. Fish & Wildlife Service, California Department of Fish and Game, the Central Valley Regional Water Quality Control Board, Contra Costa County and Contra Costa Water District. In late 1995, environmental documentation for the first five years was completed and the Use Agreement was signed. Discharge through the project began in September In September 2001, the Use Agreement was extended for another 8 years and 3 months (through December 2009). An Environmental Impact Report/Environmental Impact Statement was completed and on September 7, 2001 the Central Valley Regional Water Quality Control Board issued new Waste Discharge Requirements. Other items completed to support the continued use were a Biological Assessment/Biological Opinion, a selenium Total Maximum Monthly Load (TMML) report submitted by the Regional Board to EPA and a continued monitoring program. The new 2001 Use Agreement contains continued reductions in selenium discharge until ultimately TMML limits are achieved in 2005 for above normal and wet years and continued progress is made to meet water quality objectives in 2010 for below normal, dry and critical years. The new Use Agreement also includes salinity reductions.

30 28 GRASSLAND BYPASS PROJECT In 2007 negotiations renewed to extend the Use Agreement for a period of time up to December 2019 to allow the final measures to be implemented to reduce the discharge of sub-surface drainage water from the Grassland Drainage Area. An EIS/EIR was completed for the time extension. CEQA for the project was adopted on October 8, A biological opinion was issued on December 18, 2009 and the USBR adopted the Record of Decision on December 21, The Central Valley Regional Water Quality Control Board adopted a Basin Plan Amendment incorporating a delay in meeting Mud Slough selenium standards on May 27, 2010 and this Basin Plan was approved by the State Water Resources Control Board on October 5, This Basin Plan was subsequently approved by the State Office of Administrative Law. Steps ongoing include coordination with the Oversight Committee for the Use Agreement and the Regional Water Quality Control Board for issuance of new Waste Discharge Requirements. In July 2015 New Waste Discharge Requirements were adopted. Figures 2a through 2e show the monthly discharges from the Grassland Bypass Project from WY 1997 through the end of calendar year In August 2005 the Grassland Basin Drainers formally requested revisions to the selenium load values for selenium. This puts the load values in the Use Agreement in step with the load values in the Waste Discharge Requirements, which include setting the TMML for four different year types (wet, above normal, dry/ below normal and critical). Annual discharges compared to load limits are shown on Figure 3. Future load limits are also shown. Table 1 sets forth discharges from the Grassland Drainage Area for the period Water Year 1996 through Water Year The Grassland Bypass Project began in Water Year Water Year 2012 was a dry year type and Water Years 2013 and 2014 were critical year types in the San Joaquin. These year types affect the discharge from the Grassland Bypass Project, both in terms of the TMML Load Allocation (more is allowed in wetter years) and in actual discharge (the discharged loads tend to be higher in wet year types). The discharge has been reduced significantly since before the project began in Water Year 1995 as follows: A selenium load reduction of 94% in 2012, 95% in 2013, and 97% in 2014 (compared to the Water Year 1995 pre-project discharge). A salt load reduction of 84% in 2012,77% in 2013, and 81% in A boron load reduction of 72% in 2012,64% in 2013, and 72% in 2014 An overall discharge reduction of 82% in 2012, 82% in 2013, and 88% in The 5 ppb 4-day average selenium water quality objective at Crows Landing was met at all times in 2012 through In WY 1996, prior to the Grassland Bypass Project, the mean selenium concentration in Salt Slough at Lander Avenue was 16 parts per billion (ppb). The 2 ppb monthly mean water quality objective for Salt Slough was met in all months in WY 2012 through In WY 1996 the monthly mean selenium concentration at Camp 13 Ditch was 55.9 parts per billion (ppb). Selenium levels in the Camp 13 and the Agatha Canal did not exceed the 2 ppb monthly threshold at any time in 2012 through 2014 when deliveries to Grassland Water District were being made. SAN JOAQUIN RIVER WATER QUALITY IMPROVEMENT PROJECT In 2001, funds provided from Proposition 13 allowed for the purchase and improvement of 4,000 acres of land within the Grassland Drainage Area as part of the San Joaquin River Water Quality Improvement Project (SJRIP) for the purpose of drain water disposal. The location of the SJRIP Project is shown in Figure 1 and the cropping details for WY 2012 through WY 2014 are shown in Figure 4a, 4b, and 4c (respectively). The first phase of the SJRIP was implemented in the winter of WY 2001 with the planting of salt tolerant crops and construction of distribution facilities. In 2007, with funding from California s Proposition 50, an additional 2,000 acres of reuse area was purchased, and funding from Reclamation was used to develop the land to salt tolerant crops. Since the project s inception, the planted acreage has increased from the original 1,821 acres to more than 5,200 acres, which have been irrigated with drainage water or blended water. In 2012, 23,700 acre feet of drain water was applied to the project, reusing 3,300 pounds of selenium, 118,00 tons of salt, and 545,000 pounds of boron. By 2014 that amount rose to almost 31,000 acre feet, reusing 3,711 pounds of selenium, 179,600 tons of salt, and almost 880,000 pounds of boron.

31 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 29 The SJRIP project is the key for the Grassland Drainage Area as a whole to meet future selenium load limits. Future phases call for development of the additional acreage, installation of subsurface drainage systems and implementation of treatment and salt disposal components. A tiered contaminant monitoring program is a part of the SJRIP projects is the fourteenth year of bird egg monitoring at the project site. In 2014, avian monitoring continued and included the numbers and nesting outcomes of killdeer, black-necked stilts, and American avocets; and the selenium, boron, and mercury content of eggs of killdeer, black-necked stilts, American avocets, and red-winged blackbirds nesting in the project area and on a mitigation site. The collection of reference area samples that began in 2002 for killdeer and in 2003 for recurvirostrids (black-necked stilt and American avocet, combined) and red-winged blackbirds was discontinued in 2014 because more than 10 years of data were judged sufficient to establish selenium and boron exposure in the project vicinity. In addition to avian monitoring, a tiered program for monitoring contaminants, designed to detect potential exposure of San Joaquin kit foxes to selenium by monitoring selenium levels in vegetation and small mammals, was conducted for the fifth year in the eastern and western project areas. To protect shorebirds from project-related impacts measures have been implemented since 2006 to discourage shorebirds from foraging and nesting on the project site. The Panoche Drainage District has hazed shorebirds from the project site, modified open drains to deter shorebirds from using traditional nest sites, and installed a mitigation site to provide an alternative clean-water nesting habitat. To further prevent nesting on the project site, 8.5 miles of drain have been filled, and 2.4 miles of drain have been narrowed since In 2014, in the eastern project area, habitat modifications combined with hazing reduced shorebird nesting attempts to zero for recurvirostrids (See Figure 5) and to 10 for killdeer. Neither killdeer nor recurvirostrids were detected nesting in the western project area in Eggs were collected for three avian species groups: killdeer, red-winged backbird, and recurvirostrids. Five killdeer and 11 red-winged blackbird eggs were collected from the eastern project area (there were no recurvirostrid nests in the eastern project area), and five recurvirostrid eggs were collected form the mitigation site. All collected eggs were analyzed for selenium and boron concentrations. Full details and monitoring results of the tiered contaminant monitoring program for 2012, 2013 and 2014 can be found on the project website at: OTHER ACTIVITIES Figure 6 shows an estimate of the impact of control activities that occurred during Water Year Conservation, which includes improved irrigation application, tiered water pricing and tailwater controls accounted for a reduction of approximately 7,600 pounds of selenium from historic loads in Reuse and treatment, which includes recycling, use of subsurface drainage water on salt tolerant crops and displacement of subsurface drainage water such as for wetting of roadways for dust control, resulted in a 4,300 pounds reduction Water Year Discharge to the San Joaquin River through the Grassland Bypass Project was 800 pounds in WY Figure 7 shows the same data for WY 2013: Conservation of approximately 7,700 pounds; Reuse and treatment of approximately 4,400 pounds; and discharge to the San Joaquin River of approximately 600 pounds. Figure 8 shows the WY 2014 data: Conservation of approximately 6,800 pounds; Reuse and treatment of approximately 5,600 pounds; and discharge to the San Joaquin River of approximately 300 pounds. The Grassland Area Farmers and member districts are continuing advances into drainage management and disposal with the cooperation of federal and state agencies. Continued funding is being sought for these activities.

32 30 GRASSLAND BYPASS PROJECT Tables Table 1. Discharges from the Grassland Drainage Area for the period Water Year 1996 through Water Year Table 2. Figures Figure 1. Grassland Bypass Project Location Map Figure 2a. Discharge from the Grassland Bypass Project Figure 2b. Discharge from the Grassland Bypass Projec Figure 2c. Discharge from the Grassland Bypass Project Figure 2d. Discharge from the Grassland Bypass Project Figure 2e. Discharge from the Grassland Bypass Project Figure 3. Grassland Drainage Area Selenium Discharge and Targets Figure 4a. Cropping Details WY 2012 Figure 4b. Cropping Details WY 2013 Figure 4c. Cropping Details WY 2014 Figure 5. Recurvirosrtid Nesting Pairs Figure Drainage Management Historic Drainage Water (lbs selenium) Figure Drainage Management Historic Drainage Water (lbs selenium) Figure Drainage Management Historic Drainage Water (lbs selenium)

33 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 31 TABLE 1. DISCHARGES FROM THE GRASSLAND DRAINAGE AREA FOR THE PERIOD WATER YEAR 1996 THROUGH WATER YEAR WATER YEAR DISCHARGE (ACRE FEET) SELENIUM LOAD (LBS) BORON LOAD (LBS) SALT LOAD (TONS) ,600 11, , , ,000 10, , , ,900 7, , , ,300 9, , , ,300 5, , , ,300 4, , , ,300 4, , , ,400 3, , , ,300 4, , , ,700 3, , , ,000 4, , , ,000 3, , , ,500 2, ,000 79, ,700 1, ,000 66, ,200 1, ,000 55, ,500 1, ,000 67, ,500 2, ,000 87, , ,000 38, , ,000 54, , ,000 44,834 % Reduction % 94% 72% 84% % Reduction % 95% 77% 68% % Reduction % 97% 72% 81%t

34 32 GRASSLAND BYPASS PROJECT TABLE 2 WATER YEAR REUSED DRAIN WATER (ACRE FEET) DISPLACED SELENIUM (POUNDS) DISPLACED BORON (POUNDS) DISPLACED SALT (TONS) , NA 4, , NA 10, , NA 7, ,850 1,025 61,847 14, ,711 1,119 77,134 17, ,376 1, ,299 27, ,890 2, ,956 41, ,143 2, ,627 40, ,139 2, ,289 51, ,233 3, ,582 61, ,955 3, ,435 80, ,595 2, ,362 60, ,119 3, ,752 75, ,623 4, , , ,735 3, , , ,170 3, , , ,870 3, , ,560 NA = Not Available PDD drainage reuse project prior to SJRIP

35 FIGURE 1. GRASSLAND BYPASS PROJECT LOCATION MAP CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 33

36 34 GRASSLAND BYPASS PROJECT FIGURE 2a. DISCHARGE FROM THE GRASSLAND BYPASS PROJECT OCTOBER 1996 THROUGH SEPTEMBER SELENIUM Lbs OCT JAN APR JULY OCT JAN APR JULY OCT JAN APR JULY OCT JAN APR JULY OCT JAN APR JUL Lbs OF SELENIUM DISCHARGED TARGET FIGURE 2b. DISCHARGE FROM THE GRASSLAND BYPASS PROJECT October 2001 through December Beginning of Phase III 3 Month Transition SELENIUM Lbs OCT DEC FEB APR JUN AUG OCT DEC FEB APR JUN AUG OCT DEC FEB APR JUN AUG OCT DEC FEB APR JUN AUG OCT DEC 0 Lbs OF SELENIUM DISCHARGED TARGET

37 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 35 FIGURE 2c. DISCHARGE FROM THE GRASSLAND BYPASS PROJECT January 2005 through December SELENIUM Lbs JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV 0 Lbs OF SELENIUM DISCHARGED TARGET FIGURE 2d. DISCHARGE FROM THE GRASSLAND BYPASS PROJECT January 2009 through December SELENIUM Lbs JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV 0 Lbs OF SELENIUM DISCHARGED TARGET

38 36 GRASSLAND BYPASS PROJECT FIGURE 2e. DISCHARGE FROM THE GRASSLAND BYPASS PROJECT January 2013 through December SELENIUM Lbs JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV JAN MAR MAY JUL SEP NOV 0 Lbs OF SELENIUM DISCHARGED TARGET FIGURE 3. GRASSLAND DRAINAGE AREA SELENIUM DISCHARGE AND TARGETS Begin Grassland Bypass Project Se Discharge (lbs) Water Year Calendar Year Begin 2001 Use Agreement Load Limits Begin Use Agreement TMML Load Alllocation to meet Water Quality Objectives in the SJR at Crows Landing Actual Discharge from Drainage Area 0 Water Year and Type

39 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 37 FIGURE 4a. CROPPING DETAILS WY 2012 RP-4 W W-16 Central Pump Station W W BL D N H RP-5 2F Q1 2R1 BL Main Drain Connection Fresno County Merced County W A1 Lorenzetti Pump RP-3 RP-2 RP N1 W-14 BL BL Existing Distribution Canal 15-1 W R1 Middle Pump Station W W W W-2 W R1 W R1 11J1 BL W-5 W RL W-6 13R BL W-11 W A1 RP-9 18Q1 W-13 LEGEND SJRIP-1 SJRIP-2 Fenced Areas (1454 Acres) ACREAGE ACREAGE CROP Tiled Fields (1677 Acres) Alfalfa Reuse Area Boundary Bermuda Fallow Proposed Drainage Distribution Pump Station PROJECT 2012 CROP MAP Field-row Crops Proposed Drainage Distribution Pipeline FRESNO COUNTY Jose Tall Wheatgrass Pasture Existing Regional Drain North PANOCHE WATER DISTRICT 10 0 Paspalum Delivery System Scale of Miles FIREBAUGH CALIFORNIA 38 0 Pistachio Trees O'BANION PROPERTY 0 1 FEBRUARY Not to be Developed BL Bio Liven Total Acres SAN JOAQUIN RIVER IMPROVEMENT

40 38 GRASSLAND BYPASS PROJECT FIGURE 4B. CROPPING DETAILS WY 2013 RP W Main Drain Connection A Middle Pump Station RL Crooked Pump Station RP-4 RP-3 W Central Pump 31-1 Station W RP-1 3D1 3N1 3H1 RP-5 2F1 3Q1 2R1 W-4 Lorenzetti Pump 10N1 Existing Distribution Canal 15-1 W R1 W W W W W-2 W R R1 11J W-5 W-6 13R1 18A1 RP-9 18Q1 W-13 SAN JOAQUIN RIVER IMPROVEMENT PROJECT 2013 CROP MAP FRESNO COUNTY PANOCHE WATER DISTRICT North FIREBAUGH CALIFORNIA Scale of Miles JUNE Merced County Fresno County

41 FIGURE 4C. CROPPING DETAILS WY 201 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 39

42 40 GRASSLAND BYPASS PROJECT FIGURE 5. RECURVIROSRTID NESTING PAIRS Number of Pairs Recurvirosrtid Nesting Pairs Year FIGURE DRAINAGE MANAGEMENT HISTORIC DRAINAGE WATER (LBS SELENIUM 7,600 Conservation lbs Selenium conserved through GAF activities. Improved irrigation applications Tiered water pricing Tailwater controls Tradable Loads 57,000 AF 12,700 lbs Se 240,000 Tons Salt 800 River Discharge lbs Selenium discharged through the GBP 2012 Drainage Management 4,300 Reuse & Treatment lbs Selenium reused, recycled or treated. Recycling Use on salt tolerant crops Displacement Pilot Treatment

43 CHAPTER 2: DRAINAGE CONTROL ACTIVITIES BY THE GRASSLAND AREA FARMERS 41 FIGURE DRAINAGE MANAGEMENT HISTORIC DRAINAGE WATER (LBS SELENIUM 7,700 Conservation lbs Selenium conserved through GAF activities. 57,000 AF 12,700 lbs Se 240,000 Tons Salt Improved irrigation applications Tiered water pricing Tailwater controls Tradable Loads 600 River Discharge lbs Selenium discharged through the GBP 4,400 Reuse & Treatment lbs Selenium reused, recycled or treated. Recycling Use on salt tolerant crops Displacement Pilot Treatment 2013 Drainage Management FIGURE DRAINAGE MANAGEMENT HISTORIC DRAINAGE WATER (LBS SELENIUM) 6,800 Conservation lbs Selenium conserved through GAF activities. Improved irrigation applications Tiered water pricing Tailwater controls Tradable Loads 57,000 AF 12,700 lbs Se 240,000 Tons Salt 300 River Discharge lbs Selenium discharged through the GBP 5,600 Reuse & Treatment lbs Selenium reused, recycled or treated. Recycling Use on salt tolerant crops Displacement Pilot Treatment 2014 Drainage Management

44 42 GRASSLAND BYPASS PROJECT

45 CHAPTER 3: FLOW AND SALINITY MONITORING FLOW AND SALINITY MONITORING Michael C. S. Eacock 1 Jeffrey Papendick 2 1 Project Manager/Soil Scientist, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California Telephone: (559) meacock@usbr.gov 2 Natural Resource Technician, US Bureau of Reclamation, South-Central California Area Office, 1243 N Street, Fresno, California jpapendick@usbr.gov SUMMARY Flow and electrical conductivity (EC) are measured to monitor the effects of the Grassland Bypass Project (GBP) on the San Luis Drain, Mud Slough, Salt Slough, and the San Joaquin River. The U.S. Geological Survey (USGS) measured flow and EC at five monitoring stations (D, F, G, H, and N). The San Luis & Delta-Mendota Water Authority (Authority) measured flow and EC in the San Luis Drain at Station A and B2. The Bureau of Reclamation (Reclamation) measured the EC of water quality samples collected at Station B/B3 and in wetlands water supply channels (Stations C, J, and K). The San Francisco Estuary Institute compiled this information in monthly and quarterly reports. Figure 1 is a map that shows the location of the monitoring stations along the San Luis Drain and tributaries of the San Joaquin River. Figure 2 is a schematic diagram of the Project with the location of monitoring sites discussed in this report. Table 1 is a summary of how flow and salinity are measured at Stations A, B2, C, D, F, G, and N. Tables 2-8 list average monthly flows, flow-weighted EC measurements, and salt loads in water passing the seven stations from January 2012 through December Table 9 lists the average monthly EC of water in the Grasslands wetlands supply channels and the San Joaquin River. Figure 3 in Chapter 1 shows the pattern of rainfall and discharge from the Grassland Drainage Area (GDA) for 2012 through Note the minor increases in flow following winter rainstorms and minimal flows during summer months. STATION A - SAN LUIS DRAIN NEAR SOUTH DOS PALOS, CALIFORNIA GRASSLAND BYPASS PROJECT STATION A Location Agency ID Responsibility San Luis Drain Check 17, near South Dos Palos, California Regional Board MER562 Formerly USGS San Luis & Delta-Mendota Water Authority (Panoche Drainage District) Parameters Equipment Stage, electrical conductivity, temperature Sharp-crested weir, stilling well with a Stevens recorder and shaft encoder, staff gauge, weir stick; electrical conductivity/temperature sensor; data logger.

46 44 GRASSLAND BYPASS PROJECT Description Station A is located near South Dos Palos, California. Its purpose is to measure the volume and quality of agricultural drain water from the Grassland Drainage Area (GDA) as it enters the San Luis Drain from the Grassland Bypass Channel. Data Summary Table 2 summarizes the monthly flow and salinity of water that passed Station A from January 2012 to December The total flow for this period was 22,445 acre-feet. The average flow rate was 10.3 cfs with a daily maximum of 97.7 cfs on December 14, The monthly average flow-weighted EC of water was about 6,170 microsiemens per centimeter (μs/cm). We estimate that this water contained 130,200 tons of salts. STATION B2 - SAN LUIS DRAIN NEAR GUSTINE, CALIFORNIA GRASSLAND BYPASS PROJECT STATION B2 Location Terminus of the San Luis Drain Agency ID Formerly Regional Board MER535, USGS Responsibility Parameters Equipment San Luis & Delta-Mendota Water Authority (flow, EC, temp) Reclamation (Weekly field measurements of EC at Station B3) Stage, velocity, electrical conductivity, temperature Sharp-crested weir, stilling well with a Stevens recorder and shaft encoder, staff gauge, weir stick; electrical conductivity/temperature sensor; data logger Description Station B2 is located about 24 miles northwest of Station A at the terminus of the Drain. It is the primary site for measuring the flow and selenium load discharged from the GDA into Mud Slough. The performance of the GBP to manage flows and selenium loads is assessed at this site. Measurements of flow and EC were taken by the San Luis and Delta-Mendota Water Authority at Station B2. Reclamation measured EC in grab samples and daily composite samples collected from the Drain at the Gun Club Road bridge about two and a half miles upstream from the terminus (Station B3). Data Summary Tables 3 summarizes the monthly flow and salinity of water that passed Station B2 from January December The total flow of water passing Station B was 28,330 acre-feet at an average rate of 13.0 cfs. Peak daily flow was cfs on December 14, 2012 following a rainstorm. The monthly average flow-weighted EC of water passing Site B was 6,216 μs/cm. The total load of salt discharged to Mud Slough is estimated to be 153,360 tons. STATION C - MUD SLOUGH (NORTH), UPSTREAM OF SAN LUIS DRAIN DISCHARGE GRASSLAND BYPASS PROJECT STATION C Location Agency ID Responsibility Parameters Equipment Mud Slough, approximately 1/2 mile upstream of San Luis Drain terminus Formerly Regional Board MER536 Reclamation (Weekly field measurements of EC) Electrical conductivity, temperature, ph, boron None

47 CHAPTER 3: FLOW AND SALINITY MONITORING 45 Description Station C is located in Mud Slough upstream from the end of the San Luis Drain. Water at this monitoring station derives primarily from managed wetlands in the North and South Grassland Water District and the Kesterson National Wildlife Refuge. Data collected at this site are considered as the baseline for measuring the impact of the GBP on the slough. Reclamation measured EC in weekly grab samples. Data Summary Table 4 summarizes the monthly flow and salinity of water that passed Station C. Flow was not measured at this site, but was estimated as the difference between flows passing Stations D and B. We estimate that 107,975 acre-feet of water flowed past this site. The average flow was 50 cfs with a daily maximum of cfs on December 15, The average monthly EC of water was 1,776 μs/cm, and the total salt load is estimated to have been more than 152,380 tons. Reclamation did not collect samples from this site between October and December 2013 or when flow was insufficient. STATION D - MUD SLOUGH NEAR GUSTINE, CALIFORNIA, DOWNSTREAM FROM THE SAN LUIS DRAIN DISCHARGE GRASSLAND BYPASS PROJECT STATION D Location Agency ID Responsibility Parameters Equipment Mud Slough near Gustine, California USGS Formerly Regional Board MER542 US Geological Survey (flow, EC, temp) Reclamation (Weekly field measurements of EC) Stage, electrical conductivity, temperature Pressure transducer, electrical conductivity/temperature sensor, data logger, satellite link. Description Station D is located in Mud Slough about one-quarter mile downstream from the terminus of the SLD. Data Summary Table 5 summarizes the monthly flow and salinity of water that passed Station D from January 2012 to December We estimate that 136,980 acre-feet flowed past this site. The flow from the San Luis Drain was 21 percent of this volume. The average flow rate was 63 cfs, with a maximum of 447 cfs on December 15, The monthly average flow-weighted EC of water was 3,391 μs/cm. We estimate that 340,730 tons of salt passed this site, of which 45 percent were from the San Luis Drain. STATION F - SALT SLOUGH AT HIGHWAY 165 (LANDER AVENUE) GRASSLAND BYPASS PROJECT STATION F Location Agency ID Responsibility Parameters Equipment Salt Slough at Highway 165 near Stevinson, California USGS Formerly Regional Board MER531 US Geological Survey Reclamation (Weekly field measurements of EC) Stage, electrical conductivity, temperature Pressure transducer, electrical conductivity/temperature sensor, data logger, cellular telephone and modem.

48 46 GRASSLAND BYPASS PROJECT Description Station F is where flow and water quality are monitored in Salt Slough, an important channel for supplying water to local wildlife refuges. The GBP has removed most of the agricultural drainage water from Grassland wetland supply channels. The water in Salt Slough is largely derived from wetlands in the Los Banos Wildlife Area, and the San Luis National Wildlife Refuge Complex. Data Summary Table 6 summarizes the monthly flow and salinity of water that passed Station F between January 2012 and December We estimate that 228,530 acre-feet of water passed the site at an average rate of 105 cfs. The highest daily flow was 264 cfs on March 20, The monthly average flow-weighted EC of water was about 1,401 μs/cm, and we estimate the total load of salt in the water to have been 301,580 tons. There were no discharges of agricultural drainage water from the GDA into the Grasslands wetlands water supply channels. STATION G - SAN JOAQUIN RIVER AT FREMONT FORD, CALIFORNIA GRASSLAND BYPASS PROJECT STATION G Location Agency ID Responsibility Parameters Equipment San Joaquin River at Fremont Ford, California USGS Formerly Regional Board MER538 US Geological Survey (flow, EC, temp) Reclamation (Weekly field measurements of EC) Stage, electrical conductivity, temperature Design Analysis CO2 bubbler pressure transducer, electrical conductivity/temperature sensor, data logger, GOES transmitter. Description Station G is located along the San Joaquin River next to the Highway 140 bridge, about five miles northeast of Gustine, California. It is about two miles upstream from the confluence of the river and Mud Slough. This site is used to measure the baseline flows and quality of water in the River before it receives water from the GBP. Data Summary Table 7 summarizes the monthly flow and salinity of water that passed Station G between January 2012 and December The amount of water that passed this site was 309,530 acre-feet at an average rate of 143 cfs. The highest flow of 1,210 cfs occurred on December 29, The average EC of water was about 1,584 μs/cm. We estimate that about 436,090 tons of salt passed this site. STATION N - SAN JOAQUIN RIVER AT CROWS LANDING, CALIFORNIA Location Responsibility Parameters Equipment GRASSLAND BYPASS PROJECT STATION N San Joaquin River at Crows Landing, California (USGS ) (Regional Board STC504) US Geological Survey (flow, EC, temp) Reclamation (Daily composite EC, Weekly field measurements of EC) Stage, electrical conductivity, temperature Design Analysis CO2 bubbler pressure transducer, electrical conductivity/temperature sensor, data logger, cellular telephone and modem. Description Station N is located at Crows Landing on the San Joaquin River, about eleven miles downstream of the tributary of the Merced River.

49 CHAPTER 3: FLOW AND SALINITY MONITORING 47 Data Summary Table 8 summarizes the monthly flow and salinity of water that passed Station N between January 2012 and December The amount of water that passed this site was about 979,460 acre-feet at an average rate of 451 cfs. The highest flow of 1,960 cfs occurred on December 28 and 29, The average EC of water was 1,321 μs/cm. We estimate that 1,041,850 tons of salt were in the water that passed this point. Discharge from the GDA contributed about 3 percent of the flow and 15 percent of the salt load passing this site. Other Monitoring Stations Panoche Drainage District staff collected samples of water each week from Camp 13 Ditch, Agatha Canal, CCID San Luis Canal, and Santa Fe Canals (Stations J, K, L2, and M2, respectively) during 2012 and Sampling at Stations L2 and M2 ceased in late 2013 and sampling was reduced at Stations J and K to only when flow passing each site was over 20 cfs. It was determined that flow lower than 20 cfs does not reach Refuge channels. These samples were analyzed by the Reclamation. The purpose of these samples is to ensure that no agricultural drainage water from the GDA enters wetland supply channels in Grasslands Water District. The EC of each sample was measured in the field. Table 9 summarizes monthly average EC of water in wetland supply channels, Salt Slough, and San Joaquin River from 2012 to The data show a general increase in salinity as water passes through the southern portion of Grasslands Water District, as measured at Sites J and K, through the northern portion of Grasslands Water District at Sites L2 and M2, then into Salt Slough and the lower San Joaquin River. WEB LINKS TO USGS REAL-TIME DATA STATIONS STATION DESCRIPTION URL D Mud Slough downstream of SLD discharge F Salt Slough at HWY H G San Joaquin River at Hills Ferry San Joaquin River at Fremont Ford Tables Table 1. Summary of Flow & Salinity Monitoring Table 2. Monthly Flow and Salinity of Water Entering the San Luis Drain (Station A) Table 3. Monthly Flow and Salinity of Water in the San Luis Drain (Station B/B2) Table 4. Monthly Flow and Salinity of Water in Mud Slough Upstream of the San Luis Drain (Station C) Table 5. Monthly Flow and Salinity of Water in Mud Slough Downstream of the San Luis Drain (Station D) Table 6. Monthly Flow and Salinity of Water in Salt Slough (Station F) Table 7. Monthly Flow and Salinity of Water in San Joaquin River at Fremont Ford (Station G) Table 8. Monthly Flow and Salinity of Water in the San Joaquin River at Crows Landing (Station N) Table 9. Electrical Conductivity of Water in Grassland Wetland Supply Channels Figures Figure 1. Map of Grasslands Bypass Project and collection sites. Figure 2. Grasslands Bypass Project schematic diagram

50 48 GRASSLAND BYPASS PROJECT TABLE 1. SUMMARY OF FLOW & SALINITY MONITORING STATION AGENCY PARAMETER SAMPLE FREQUENCY A EC TO TDS CONVERSION FACTOR (1) SLDMWA Flow Continuous SLDMWA EC Continuous 0.74 SLDMWA/ BOR B/B3 Reclamation EC B2 C D F G N EC Weekly composite of daily samples Daily composite samples and weekly grab samples SLDMWA Flow Daily average EC Daily average 0.74 USGS Flow Monthly BOR Flow Calculated (2) BOR EC Weekly grab 0.68 USGS Flow Continuous USGS EC Continuous 0.69 BOR EC Weekly grab USGS Flow Continuous USGS EC Continuous 0.68 BOR EC Weekly grab USGS Flow Continuous USGS EC Continuous 0.68 BOR EC Weekly grab USGS Flow Continuous USGS EC Continuous 0.62 BOR EC Daily composite samples BOR EC Weekly grab 0.74 (1) CVRWQCB, February Loads of Salt, Boron, and Selenium in the Grassland Watershed and Lower San Joaquin River, October September 1995 Volume I: Load Calculations. Sacramento, California (2) Difference in flow measured at Stations D and Station B2

51 CHAPTER 3: FLOW AND SALINITY MONITORING 49 TABLE 2. MONTHLY FLOW AND SALINITY OF WATER ENTERING THE SAN LUIS DRAIN (STATION A) Average cfs FLOW Total acre-feet Flow-weighted Electrical conductivity µs/cm SALINITY Total dissolved solids mg/l January ,040 3,730 2,940 Salt load tons February ,489 2,580 2,910 March ,240 4,910 3,630 6,120 April ,739 4,250 3,930 May ,605 3,410 3,340 June ,106 3,040 3,600 July ,233 3,870 4,530 August ,857 3,590 2,690 September ,721 3,490 1,090 October ,743 3,510 1,150 November ,553 3,370 1,790 December ,199 3,850 4,560 January ,323 3,940 4,130 February ,878 3,610 4,030 March ,757 3,520 4,160 April ,114 3,780 4,320 May ,571 3,380 3,360 June ,961 3,670 3,040 July ,388 4,730 5,270 August ,743 4,990 5,230 September ,475 5,530 3,230 October ,335 6,170 3,440 November ,761 5,740 2,650 December ,673 6,420 2,970 January , ,640 February ,040 6, ,930 March , ,990 April , ,860 May , ,670 June , ,980 July , ,110 August , September , October , November , ,680 December ,450 6, ,560 AVERAGE ,170 4,565 3,617 TOTAL , , , ,200 Data sources: Calculated from mean daily flow and EC data collected by San Luis & Delta-Mendota Water Authority Total acre-feet, TDS, and Salt load - calculated Note: EC - TDS conversion: 0.74

52 50 GRASSLAND BYPASS PROJECT TABLE 3. MONTHLY FLOW AND SALINITY OF WATER IN THE SAN LUIS DRAIN (STATION B/B2) Average cfs FLOW Total acre-feet Flow-weighted Electrical conductivity µs/cm SALINITY Total Dissolved Solids mg/l Salt load tons January ,672 1,980 2,560 February ,160 2,838 2,100 3,310 March ,460 3,663 2,710 5,380 April ,368 3,230 2,900 May ,774 3,530 3,170 June ,782 3,540 3,800 July ,936 3,650 3,920 August ,975 3,680 2,700 September ,657 3,450 1,920 October ,422 2,530 2,270 November ,454 2,560 3,100 December ,280 4,061 3,010 5,240 January ,150 4,575 3,390 5,300 February ,060 4,719 3,490 5,030 March ,846 3,590 4,740 April ,985 4,430 4,880 May ,964 4,410 4,260 June ,445 4,770 3,630 July ,614 4,890 5,250 August ,500 5,550 6,110 September ,772 6,490 5,120 October ,335 4,690 4,980 November ,078 3,760 3,780 December ,501 4,070 4,150 January February March April May June July August September October November December AVERAGE ,216 4,600 4,260 TOTAL , , , ,360 Data sources: Calculated from mean daily flow and EC data collected by San Luis & Delta-Mendota Water Authority Total acre-feet, TDS, and salt load - calculated Note: EC - TDS conversion: 0.74

53 CHAPTER 3: FLOW AND SALINITY MONITORING 51 TABLE 4. MONTHLY FLOW AND SALINITY OF WATER IN MUD SLOUGH UPSTREAM OF SAN LUIS DRAIN (STATION C) Average cfs ESTIMATED FLOW (*) Total acre-feet Flow-weighted Electrical conductivity µs/cm SALINITY Total Dissolved Solids mg/l Salt load tons January ,730 1,736 1,180 10,800 February ,000 2,053 1,396 9,490 March ,560 2,329 1,583 14,130 April ,380 2,709 1,842 5,960 May ,380 1,606 1,092 2,050 June ,080 1, ,680 July ,570 1, ,030 August ,510 1, ,530 September ,220 1, ,330 October ,170 1, ,890 November ,400 1,583 1,076 7,900 December ,040 1, ,750 January ,480 1,958 1,331 11,730 February ,530 2,190 1,489 9,180 March ,980 2,212 1,504 16,330 April ,190 2,556 1,738 5,180 May ,910 1,640 1,115 2,900 June ,710 1,630 1,108 2,580 July ,130 1, ,510 August , September , October ,480 NA NA NA November ,560 NA NA NA December ,040 NA NA NA January ,400 NA NA NA February ,980 NA NA NA March ,420 2,747 1,868 11,230 April ,370 3,072 2,089 3,890 May NA NA NA June NA NA NA July NA NA NA August NA NA NA September NA NA NA October ,757 1, November ,633 1,110 1,090 December ,550 1, ,640 AVERAGE 50 2,999 1,776 1,208 5,861 TOTAL 1, ,975 46,171 31, ,380 Flow - Calculated difference between Stations B and D. Data sources: EC - California Regional Water Quality Control Board, Site MER536 Total acre-feet, TDS, and salt load - calculated Note: EC - TDS conversion: 0.68

54 52 GRASSLAND BYPASS PROJECT TABLE 5. MONTHLY FLOW AND SALINITY OF WATER IN MUD SLOUGH DOWNSTREAM OF SAN LUIS DRAIN (STATION D) FLOW Average cfs Total acre-feet SALINITY Flow-weighted Electrical conductivity µs/cm Total Dissolved Solids mg/l Salt load tons January ,680 2,090 1,440 15,040 February ,150 2,635 1,820 15,220 March ,120 2,819 1,950 21,530 April ,040 3,451 2,380 9,840 May ,100 2,976 2,050 5,850 June ,870 2,846 1,960 7,650 July ,400 3,391 2,340 7,640 August ,090 2,230 1,540 4,380 September ,630 2,314 1,600 3,550 October ,980 1,564 1,080 7,310 November ,290 1,838 1,270 10,860 December ,620 1,864 1,290 18,630 January ,790 2,350 1,620 17,160 February ,590 2,702 1,860 14,140 March ,050 2,518 1,740 21,420 April ,000 3,711 2,560 10,440 May ,680 2,856 1,970 7,180 June ,260 2,558 1,770 5,440 July ,850 3,348 2,310 5,810 August ,659 3,900 5,040 September October November December January February March April May June July August September October November December AVERAGE 63 3,805 3,391 2,340 9,465 TOTAL 2, , ,076 84, ,730 Data sources: Calculated from mean daily flow and EC data collected by USGS # Total acre-feet, TDS, and salt load - calculated Note: EC - TDS conversion: 0.69

55 CHAPTER 3: FLOW AND SALINITY MONITORING 53 TABLE 6. MONTHLY FLOW AND SALINITY OF WATER IN SALT SLOUGH (STATION F) Average cfs FLOW Total acre-feet Flow-weighted Electrical conductivity µs/cm SALINITY Total Dissolved Solids mg/l Salt load tons January ,220 1,799 1,240 7,120 February ,990 1,521 1,050 17,120 March ,790 1,826 1,260 20,200 April ,460 1,681 1,160 14,920 May ,160 1, ,180 June ,890 1, ,260 July , ,990 August , ,400 September ,520 1, ,670 October ,150 1, ,360 November ,970 1, ,970 December ,700 1, ,530 January ,850 1,577 1,090 11,640 February ,230 1, ,300 March ,050 1,555 1,070 18,990 April ,330 1,483 1,020 12,940 May ,220 1, ,280 June ,900 1, ,920 July , ,350 August ,320 1, ,270 September ,290 1, ,730 October ,060 1, ,260 November ,500 1, ,130 December ,380 1,538 1,060 9,200 January ,540 1,746 1,200 7,410 February ,810 1,957 1,350 7,000 March ,600 2,149 1,480 9,260 April ,480 1,804 1,240 9,240 May ,810 1,635 1,130 4,320 June ,890 1, ,390 July ,790 1, ,780 August , ,660 September ,620 1, ,630 October ,190 1,601 1,100 1,780 November ,180 1,540 1,060 4,580 December ,380 1,686 1,160 10,070 AVERAGE 105 6,348 1, ,385 TOTAL 3, ,530 50,440 34, ,850 Calculated from mean daily flow and EC data collected by USGS # Data sources: Total acre-feet, TDS, and salt load - calculated Note: EC - TDS conversion: 0.68

56 54 GRASSLAND BYPASS PROJECT TABLE 7. MONTHLY FLOW AND SALINITY OF WATER IN SAN JOAQUIN RIVER, FREMONT FORD (STATION G) Average cfs FLOW Total acre-feet Flow-weighted Electrical conductivity µs/cm SALINITY Total Dissolved Solids mg/l Salt load tons January ,680 2,213 1,500 13,630 February ,150 1,991 1,350 25,980 March ,240 1,815 1,230 28,840 April ,840 1, ,300 May ,510 1, ,420 June ,900 1, ,530 July ,670 1, ,840 August ,480 1, ,430 September ,980 1, ,300 October ,090 1, ,450 November ,660 1, ,610 December , ,120 January ,340 1, ,040 February ,200 1,700 1,160 19,250 March ,680 1,709 1,160 26,310 April ,770 1,735 1,180 18,890 May ,670 1, ,500 June ,360 1, ,840 July ,680 1, ,460 August ,070 1, ,690 September ,240 1, ,630 October ,650 1,502 1,020 7,840 November ,750 1,474 1,000 10,540 December ,960 1,640 1,120 12,120 January ,510 1,976 1,340 11,860 February ,050 2,147 1,460 12,010 March ,860 2,242 1,520 16,250 April ,670 2,165 1,470 13,330 May ,230 2,320 1,580 6,940 June ,160 2,033 1,380 4,050 July ,930 1, ,550 August ,100 1, ,310 September ,810 1,632 1,110 2,730 October ,840 1,920 1,310 3,280 November ,820 1, ,090 December ,730 1,753 1,190 14,130 AVERAGE 143 8,598 1,584 1,077 12,114 TOTAL 5, ,530 57,033 38, ,090 Calculated from mean daily flow and EC data collected by USGS # Data sources: Total acre-feet, TDS, and salt load - calculated by USBR Note: EC - TDS conversion: average 143 1, total 309, ,090

57 CHAPTER 3: FLOW AND SALINITY MONITORING 55 TABLE 8. MONTHLY FLOW AND SALINITY OF WATER IN THE SAN JOAQUIN RIVER AT CROWS LANDING (STATION N) Average FLOW Total Flow-weighted Electrical conductivity SALINITY Total Dissolved Solids Salt load cfs acre-feet µs/cm mg/l tons January ,280 1, ,840 February ,700 1, ,730 March ,010 1,636 1,014 67,610 April ,360 1, ,780 May , ,830 June ,460 1, ,690 July ,640 1, ,610 August ,470 1, ,500 September ,690 1, ,810 October , ,730 November , ,710 December , ,620 January ,180 1, ,620 February ,090 1, ,850 March ,820 1, ,210 April ,020 1, ,230 May ,370 1, ,510 June ,690 1, ,980 July ,370 1, ,550 August ,090 1, ,680 September , ,690 October , ,540 November ,000 1, ,580 December ,630 1, ,600 January ,200 1, ,160 February ,450 1,761 1,092 33,330 March ,480 2,103 1,304 39,870 April ,730 1,634 1,013 29,930 May ,360 1,835 1,138 17,580 June ,050 1,859 1,152 9,480 July ,200 1,711 1,061 6,060 August ,080 1, ,110 September ,560 1, ,200 October , ,510 November , ,540 December ,470 1, ,580 AVERAGE ,207 1, ,940 TOTAL 16, ,460 47,539 29,474 1,041,850 Data sources: Calculated from mean daily flow and EC data collected by USGS # Total acre-feet, TDS, and salt load - calculated Note: EC - TDS conversion: 0.62

58 56 GRASSLAND BYPASS PROJECT TABLE 9. ELECTRICAL CONDUCTIVITY OF WATER IN GRASSLAND WETLAND SUPPLY CHANNELS GBP STATION: J K L2 M2 C F G CVRWQCB SITE ID: GWD GWD PWD PWD USBR USGS USGS Camp 13 µs/cm Agatha Canal µs/cm San Luis Canal d/s of Splits µs/cm Santa Fe Canal d/s of Splits µs/cm Mud Slough above San Luis Drain µs/cm Salt Slough µs/cm San Joaquin River at Fremont Ford µs/cm January ,090 1,276 1,736 1,799 2,213 February ,461 1,578 2,053 1,521 1,991 March ,988 2,053 2,238 2,329 1,826 1,815 April ,004 1,592 2,264 2,180 2,709 1,681 1,366 May ,606 1,213 1,409 June ,616 1,090 1,394 1,115 1,286 July ,676 1,132 1, ,109 August , , ,078 September ,175 1,101 1,363 October ,268 1,278 1,443 November ,583 1,327 1,405 December ,118 1,406 1, January ,108 1,090 1,958 1,577 1,170 February ,413 1,215 2,190 1,416 1,700 March ,436` 2,325 1,928 2,212 1,555 1,709 April , ,046 2,556 1,483 1,735 May ,640 1,190 1,362 June ,570 1,258 1,630 1,209 1,373 July , ,034 1,242 1, ,188 August , ,192 1,059 1,180 September , ,044 1,169 1,374 October NA NA 1,234 1,323 1,502 November NA NA 1,613 1,340 1,474 December NA NA 1,992 1,538 1,640 January NA NA 2,481 1,757 1,985 February NA NA NA 2,869 1,962 2,151 March 2014 NA NA NA NA 2,807 2,166 2,263 April 2014 NA NA NA NA 3,310 1,818 2,228 May 2014 NA NA NA NA 5,527 1,637 2,313 June 2014 NA NA NA NA 6,814 1,364 2,042 July 2014 NA NA NA NA NA 1,050 1,577 August 2014 NA NA NA NA NA 923 1,221 September NA NA NA 1,099 1,670 October NA NA 1,722 1,203 1,962 November NA NA 1,672 1,555 1,466 December NA NA 1,457 1,718 1,769 Data source: Annual average electrical conductivity calculated from weekly grab samples collected by Panoche Water District and USBR and real time sensors monitored by Grasslands Water District and the USGS

59 FIGURE 1. MAP OF THE GRASSLAND BYPASS PROJECT CHAPTER 3: FLOW AND SALINITY MONITORING 57

60 58 GRASSLAND BYPASS PROJECT FIGURE 2. GRASSLAND BYPASS PROJECT - SCHEMATIC DIAGRAM SHOWING LOCATIONS OF GBP MONITORING SITES RELATIVE TO MAJOR HYDROLOGIC FEATURES OF THE STUDY AREA N Merced River H (Seasonal) Mud Slough (north) E I D C B G San Luis Drain San Joaquin River F Salt Slough Fremont Canal San Luis Canal Santa Fe Canal San Luis Canal North Grassland Water District L2 M2 Santa Fe Canal San Luis Drain Blake-Porter Bypass Wetland water supply Camp 13 Canal South Grassland Water District J K Agatha Canal A Grassland Bypass Main Canal (via DMC and Mendota Pool) Agricultural Water Districts

61 04 WATER CHAPTER 4: WATER QUALITY MONITORING 59 QUALITY MONITORING Michael C. S. Eacock 1 Jeffrey E. Papendick 2 1 Project Manager/Soil Scientist, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California Telephone: (559) meacock@usbr.gov 2 Resources Management Technician, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California jpapendick@usbr.gov INTRODUCTION The monitoring program for the Grassland Bypass Project (GBP), including water quality monitoring, is described in detail in the Compliance Monitoring Program for the Use and Operation of the Grassland Bypass Project, Phase II (USBR et. al., 2002). This chapter provides a summary of the water quality monitoring program and water quality trends for the tenth, eleventh, and twelfth years of operation of Phase II of the GBP (January 1, 2012 to December 31, 2014). Detailed water quality data of individual monitoring stations will not be provided in this summary. This information is presented by the San Francisco Estuary Institute (SFEI) in annual narrative and graphical summary reports (SFEI, 2012; SFEI, 2013; and SFEI, 2014). MONITORING PROGRAM The U.S. Bureau of Reclamation (Reclamation) is responsible for conducting water quality sampling for the GBP monitoring program. Samples are collected by field staff, when conditions permit, on a weekly basis at stations F, B/ B3, C, D, I2, G, and N. Reclamation began sampling station R, the San Joaquin River at China Island, in November The Panoche Water District (under contract with the San Luis & Delta-Mendota Water Authority) assisted Reclamation by collecting samples weekly at stations A, J, K, L2, and M2 until late The samples are then transferred to Reclamation field staff for processing and inclusion in the weekly sampling batch. Reclamation s quality assurance (QA) specialist incorporates QA samples for each sampling batch. The samples are analyzed by laboratories contracted to Reclamation. All data is reviewed and validated by the QA specialist before publication. Table 1a provides a summary of the current monitoring program. In late 2013, stations L2, and M2 were discontinued and sampling at stations J and K were reduced to when flow is over 20 cfs. Also in late 2013, in preparation for a new Waste Discharge Requirement from the Regional Water Quality Control Board, Reclamation revised the GBP monitoring programing before reverting back to the original monitoring program in early Changes in the monitoring plan are in Tables 1b and 1c. MONITORING OBJECTIVES The water quality monitoring program was designed to provide data for evaluating compliance with commitments in the Project Waste Discharge Requirements, the Use Agreement, and associated documents. The commitments include: Monthly and annual selenium load limits on discharges No degradation of the San Joaquin River water quality relative to the pre-project condition Cessation of discharge of agricultural subsurface drainage to the wetland channels Management of flows in the San Luis Drain (SLD) so as to not mobilize channel sediments

62 60 GRASSLAND BYPASS PROJECT The Monitoring Program was also designed to verify the validity of assumptions expressed in documents associated with the GBP. The assumptions include: The GBP is expected to result in selenium concentrations less than 2 µg/l in approximately 93 miles of wetland water supply channels. The increased frequency of exceeding selenium water quality objectives in Mud Slough (north) will be offset by a reduction of exceedances in Salt Slough. In addition, the Monitoring Program was intended to provide data to be used to assess spatial and temporal trends in water quality parameters of concern and to characterize habitats in which biological samples were collected. SAMPLING LOCATIONS Monitoring was conducted in four areas: the SLD, Mud Slough (north), the San Joaquin River, and the Grassland wetland water supply channels, including Salt Slough. Table 1a and 1c summarizes the Monitoring Program, and sampling locations are depicted in Figure 2 in Chapter 1. FREQUENCY OF SAMPLING The frequency of sampling is outlined in Table 1a, 1c for revised monitoring plan. Weekly composite samples were collected at station A (inflow to the SLD). Daily composite samples were collected at station B (discharge from the SLD), and at station N (San Joaquin River at Crows Landing). At station A, daily samples were composited into a weekly sample to be used along with continuous flow data to calculate weekly selenium load inflow to the SLD. As of late November 2013, station A samples were analyzed as daily samples rather than weekly composites. At station B, daily composite samples along with continuous flow data were used to calculate daily selenium load discharge into Mud Slough (north). At station N, daily composite samples were collected in order to calculate loads and evaluate compliance with Basin Plan water quality objectives. Compliance at station N for the selenium water quality objective is 5µg/L over a 4-day period for all water year types. Since the objective is based on a 4-day average concentration, consecutive daily samples are required at this station. The remaining stations were sampled on a weekly basis. Table 2 shows the summary of the selenium water quality objectives and compliance time table for Mud Slough as well as the San Joaquin River from the Mud Slough Confluence to the Merced River. SAMPLING METHODOLOGY Three types of sampling techniques were utilized, depending on the frequency of sampling and data needs: auto-sampler, mid-channel depth-integrated, and grab sample from channel bank. Auto-samplers were used to collect daily and weekly composite samples because of the remoteness of the station and frequency of sampling at stations A, B, and N. At stations A, B, and D, structures such as a bridge or platform over the channel permitted the collection of mid-channel, depth-integrated samples. For all other stations, a grab sample was collected from the stream bank. With respect to stream hydrology, lateral and vertical homogeneity was assumed for dissolved constituents at all sampling stations. MODIFICATIONS TO THE WATER QUALITY MONITORING PROGRAM During Phase I of the GBP a number of issues were resolved with respect to the water quality monitoring program. These modifications and clarifications to the monitoring program are discussed in previous Annual Reports (USBR, 1998 and SFEI, 1999, 2000, 2001, 2003, 2004b and 2005). WATER QUALITY TRENDS Detailed water quality data for each monitoring station are presented in the Grassland Bypass Project Annual Narrative and Graphical Summary Reports, January 2012 to December 2014 (SFEI, 2012; SFEI, 2013; SFEI, 2014). This presentation will be limited to major water quality trends and findings for the sixteenth, seventeenth, and eighteenth years of the GBP. Primary interests are selenium concentrations in the San Joaquin River and water quality trends in Mud Slough (north). Also of interest are sporadic exceedances in the wetland channels of selenium water quality objectives established in the Water Quality Control Plan for the Sacramento/San Joaquin River Basins.

63 CHAPTER 4: WATER QUALITY MONITORING 61 SAN JOAQUIN RIVER The selenium water quality objective is 5µg/L over a 4-day average. The compliance date was October 1, 2005 for above normal and wet water year types and October 1, 2010 for critical, dry, and below normal water year types. Compliance with selenium water quality objectives specified in the Basin Plan is measured at station N. Figure 1 depicts selenium concentrations in the San Joaquin River at monitoring stations G (weekly grab), and N (4-day average and weekly grab) for Station G is located at Fremont Ford, upstream of the Mud Slough (north) inflow to the San Joaquin River. Because this station is located upstream of drainage discharges from the GBP service area (except during flood events when drainage is occasionally routed to Salt Slough), selenium concentrations are generally low. Station N is located downstream of the GBP discharges conveyed by Mud Slough (north) and the Merced River inflow to the San Joaquin River. Merced River inflows dilute the upstream selenium contributions (CVRWQCB, 2002a). Data were unavailable for station N mid December 2012 to the end of January 2013, late July to late August 2013, mid to late October 2013, early to mid-january 2014, early to mi-march 2014, and early to mid-november 2014 due to auto sampler malfunction. For the months of January 2012 through December 2014, the applicable water quality objective was 5 µg/l (4-day average). Selenium concentrations remained below this performance goal for the three year period at both stations N and G. Figure 2 shows the monthly means at station N as well as the 5 µg/l objective. The Basin Plan and the GBP Waste Discharge Requirements (WDRs) prohibit discharge of selenium from agricultural subsurface drainage systems in the Grassland Watershed to the San Joaquin River in amounts exceeding 8,000-pounds per water year. Compliance is measured at station B. Daily selenium data, preliminary USGS flow data, and the load calculation methods found in CVRWQCB (1998b) indicate that the annual selenium loads measured at station B during Water Year 2012, WY 2013, and WY 2014 were 741 pounds, 639 pounds, and 314 pounds respectively, well below the 8,000-pound annual load limit for the Grassland Watershed. WETLAND CHANNELS Monthly mean selenium concentrations in the wetland channels between 2012 and 2014 are depicted in Figure 3. The monthly mean 2 µg/l selenium objective was met at Salt Slough (station F), Agatha Canal (station K), and Santa Fe Canal (station M2). Selenium concentrations were in excess of the monthly mean at San Luis Canal (station L2) in February 2012, March 2013, June 2013, and July Selenium concentrations were in excess of the monthly mean at Camp 13 (station J) in April Sampling at stations L2 and M2 were discontinued in Also in October 2013, selenium sampling was moved from station H to station R. Station R is the San Joaquin River at China Island approximately 1.3 miles downstream of the mud slough discharge. Regional Board staff conducted preliminary investigations on the potential sources of selenium, which are detailed in two separate reports (CVRWQCB, 2000 and CVRWQCB, 2002b). Primary sources of selenium to the channels were determined to be diversions from the 94,000-acre Drainage Project Area (DPA) (both storm water flows and seepage from control gates), supply water, subsurface agricultural drainage from areas outside of the DPA, tailwater and local groundwater. To address the first source, diversions from the DPA, the Grassland Area Farmers (GAF) developed a storm water management plan, and internal control gates were sealed. These actions appear to have controlled peaks of selenium previously observed during storm events. Despite the storm water management plan and control gate modifications made by the GAF, selenium concentrations have sporadically exceeded the 2 µg/l monthly mean selenium objective in the wetland channels.

64 62 GRASSLAND BYPASS PROJECT MUD SLOUGH (NORTH) Selenium concentrations observed at station D (Mud Slough (north) downstream of the SLD), from 2012 to 2014 are depicted in Figure 4. Water quality at station D is dominated by the GBP drainage discharge. Selenium concentrations tend to be lowest from fall through early winter (non-irrigation period) and highest during the irrigation period, which begins in mid-winter (pre-plant irrigation) and lasts through the summer.during 2012, the monthly average selenium concentrations at station D ranged from 1.1 µg/l in October to 11.5 µg/l in June. In comparison, the 15 µg/l performance goal, which will apply December 31, 2015 and the 5 µg/l (4-day average) selenium water quality objective, which will apply after December 31, 2019 for Mud Slough (north), are noted on Figure 4. Selenium concentrations regularly exceeded 5 µg/l at station D. During 2012, the observed concentration of selenium at station C (Mud Slough (north) upstream of the drainage discharge) remained below 5 µg/l (Figure 5). The maximum observed selenium concentration of 1.2 µg/l occurred in July 2012 in Mud Slough upstream of SLD. During 2013, the monthly average selenium concentrations at station D ranged from 1.0 µg/l in November to 11.5 µg/l in April. In comparison, the 15 µg/l performance goal, which will apply December 31, 2015 and the 5 µg/l (4-day average) selenium water quality objective, which will apply after December 31, 2019 for Mud Slough (north), are noted on Figure 4. Selenium concentrations regularly exceeded 5 µg/l at station D. During 2013, the observed concentration of selenium at station C (Mud Slough (north) upstream of the drainage discharge) remained below 5 µg/l (Figure 5). The maximum observed selenium concentration of 1.5 µg/l occurred in July 2013 in Mud Slough upstream of SLD. During 2014, the monthly average selenium concentrations at station D ranged from 0.4 µg/l in October to 34.9 µg/l on June, 26th. The maximum selenium concentration of 34.9 µg/l has been flagged as an outlier. The high concentration is likely due to minimal flows passing station D during the third-year of a severe drought. In comparison, the 15 µg/l performance goal, which will apply December 31, 2015 and the 5 µg/l (4-day average) selenium water quality objective, which will apply after December 31, 2019 for Mud Slough (north), are noted on Figure 4. Selenium concentrations regularly exceeded 5 µg/l at station D. During 2014, the observed concentration of selenium at station C (Mud Slough (north) upstream of the drainage discharge) remained below 5 µg/l (Figure 5). The maximum observed selenium concentration of 1.2 µg/l occurred in December 2014 in Mud Slough upstream of SLD. BORON WATER QUALITY OBJECTIVES Water quality objectives and monthly mean concentrations for boron in Mud Slough, Salt Slough, and the San Joaquin River for 2012, 2013, and 2014 are presented in Table 4. During 2012, exceedances of the 2.0 mg/l objective occurred at station D from March through September. Exceedances also occurred at station C in March and April. The water quality objective of 0.8 mg/l at station N was exceeded in March and April. During 2013, exceedances of the 2.0 mg/l objective occurred at station D from March through September. Exceedances also occurred at station C in March and April. The water quality objective of 1.3 mg/l for a critical year at station N was met every month during During 2014, exceedances of the 2.0 mg/l objective occurred at station D from March through August. Exceedances also occurred at station C in March, April, and May. The water quality objective of 1.3 mg/l for a critical year at station N was exceeded in February, March, and December. Sources of boron occur throughout the San Joaquin Basin and are not confined to the GBP service area (CVRWQCB, 2002). The CVRWQCB is currently conducting a separate effort to control salt and boron loading to the lower San Joaquin Basin. MOLYBDENUM WATER QUALITY OBJECTIVES Water quality objectives and monthly mean concentrations for molybdenum in Mud Slough, Salt Slough, and the San Joaquin River for 2012 through 2014 are presented in Table 5.

65 CHAPTER 4: WATER QUALITY MONITORING 63 During 2012, molybdenum concentrations were below the 19 µg/l water quality objectives in Mud Slough upstream of the SLD discharge, Salt Slough, and the San Joaquin River. Molybdenum concentrations exceeded water quality objectives in Mud Slough downstream of SLD Discharge (station D) in April of During 2013, molybdenum concentrations were below the 19 µg/l water quality objectives in Mud Slough upstream of the SLD discharge, Mud Slough downstream of the SLD discharge, Salt Slough, and the San Joaquin River. During 2014, molybdenum concentrations were below the 19 µg/l water quality objectives in Salt Slough and the San Joaquin River. Molybdenum concentrations exceeded water quality objectives in Mud Slough downstream of SLD Discharge (station D) in May and October, and in Mud Slough upstream of the SLD Discharge (station C) in October. NUTRIENT DATA CVRWQCB and Reclamation staff collected nutrient samples at stations B, C, D, G, and N. Available nutrient data for the San Luis Drain, Mud Slough (north), and the San Joaquin River are presented in Tables 6 through 10. The Primary Maximum Contaminant Level (MCL) for nitrate as N in drinking water is 10 mg/l nitrate expressed as nitrogen (CVRWQCB, 2003). Nitrate levels in samples collected at station B were at or below the MCL from 2012 through 2014 with a maximum recorded value of 10 mg/l in June Nitrate levels in samples collected at stations C, D, G, and N were below the MCL in all samples collected during 2012, 2013, and Nutrient sampling frequency was limited in 2014 due to low flow caused by drought. Freshwater aquatic life criteria for ammonia are found in CVRWQCB (2003). The threshold value for ammonia toxicity is a function of both the temperature and ph of the ambient water. Temperature and ph field measurements were taken to determine the ammonia toxicity threshold for each sample. Ammonia toxicity thresholds for 2012 were slightly exceeded at station B on July 2nd and Aug 1st, at station D on Jul 2nd, and at station G on Aug 14th. Thresholds were not exceeded at station C or station N. Ammonia toxicity thresholds for 2013 were slightly exceeded at station B on July 2nd, July 17th, and Aug 1st. Thresholds were not exceeded at stations C, D, G or N. Ammonia toxicity thresholds for 2013 were slightly exceeded at station B on May 8th and June 26th, and at station D and June 26th. Thresholds were not exceeded at stations C, G, or N Samples are collected to be analyzed for additional constituents (total Kjeldhal nitrogen, total phosphorus, and orthophosphate) in support of the development of a TMDL for oxygen demanding substances in the San Joaquin River and future nutrient criteria. CONCLUSIONS Monitoring has shown that selenium concentrations in the San Joaquin River are a function of location in the River with respect to discharge points and tributary inflows, and of the assimilative capacity of the River. The lowest selenium concentrations in the San Joaquin River are upstream of Mud Slough (north) inflows. Mud Slough (north) inflow contains relatively high concentrations of selenium. The Merced River dilutes the San Joaquin River with respect to selenium. Selenium concentrations in the San Joaquin River at station N, however, remain elevated relative to the background condition in the San Joaquin River at station G. The 2 µg/l monthly mean selenium water quality objective was exceeded in two of the wetland supply channels during 2012, and one wetland supply channel in Selenium concentrations were substantially lower than pre-project conditions for all stations. A number of sources may contribute to the exceedances of selenium water quality objectives in the wetland channels, including agricultural subsurface drainage from areas outside the GBP being discharged to the channels upstream of the wetlands.

66 64 GRASSLAND BYPASS PROJECT For most of the year, the water quality of Mud Slough (north) downstream of the SLD inflow is governed by the GBP drainage discharge and fluctuates widely. Selenium concentrations tend to be lowest from the fall through early winter (non-irrigation period) and highest during the irrigation season, which commences in mid winter (pre-plant irrigation) and lasts through the summer. Selenium concentrations regularly exceeded 5 µg/l in Mud Slough (north) downstream of the SLD inflow. Upstream of the drainage discharge, the concentration of selenium was below 2 µg/l from 2013 through Boron data from Mud Slough (north), Salt Slough, and the San Joaquin River were compared to applicable water quality objectives. There were no exceedances in the San Joaquin River or in Salt Slough from 2012 through Boron water quality objectives were exceeded during the irrigation season in Mud Slough (north) during 2012, 2013, and Sources of boron occur throughout the San Joaquin Basin and are not confined to the GBP. The CVRWQCB is conducting a separate effort to control salt and boron loading to the lower San Joaquin Basin. Molybdenum water quality objectives were met in Salt Slough, Mud Slough north upstream of SLD Discharge, and the San Joaquin River throughout 2012, 2013, and An exceedance occurred in Mud Slough north downstream of SLD discharge during April 2012 and May Nitrate concentrations were observed at or below the MCL in samples collected at station B, and were the lowest during the summer months for 2012, 2013, and Nitrate concentrations were below the MCL at stations C, D, G, and N in all samples. Ammonia levels were observed above the ammonia toxicity threshold at station B in July and August, at station D in July, and at station G in August. Thresholds were not exceeded at station C or station N during Ammonia toxicity thresholds were exceeded again in July and August 2013 at station B. In 2013, thresholds were met as stations C, G, N, and D. Ammonia toxicity thresholds for 2013 were slightly exceeded at station B on May 8th and June 26th, and at station D and June 26th. Thresholds were not exceeded at stations C, G, or N. References CVRWQCB. 1998a. The Water Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board, Central Valley Region, Fourth Edition: The Sacramento River Basin and the San Joaquin River Basin. California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB. 1998b. Loads of Salt, Boron, and Selenium in the Grassland Watershed and Lower San Joaquin River October 1985 to September Volume I: Load Calculations. California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB. 1998c. Compilation of Electrical Conductivity, Boron, and Selenium Water Quality Data for the Grassland Watershed and San Joaquin River (May September 1995), February California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB Review of Selenium Concentrations in Wetland Water Supply Channels in the Grassland Watershed, May California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB Waste Discharge Requirements No for the San Luis and Delta-Mendota Water Authority and the United States Department of the Interior, Bureau of Reclamation, Grassland Bypass Channel Project (Phase II ), Fresno and Merced Counties. Sacramento, CA. CVRWQCB. 2002a. Water Quality of the Lower San Joaquin River: Lander Avenue to Vernalis October September 2000 (Water Years 1999 and 2000). California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB. 2002b. Review of Selenium Concentrations in Wetland Water Supply Channels in the Grassland Watershed, April California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. CVRWQCB A Compilation of Water Quality Goals, August California Regional Water Quality Control Board, Central Valley Region. Sacramento, CA. DWR California Cooperative Snow Surveys. Chronological Reconstructed Sacramento and San Joaquin Valley Water Year Hydrologic Classification Indices. WSI HIST (11/20/ ). San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report, October I, 1997 to September 30, Richmond, CA. San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report Richmond, CA. San Francisco Estuary Institute. May Grassland Bypass Project Annual Report Richmond, CA. San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report Richmond, CA.

67 CHAPTER 4: WATER QUALITY MONITORING 65 San Francisco Estuary Institute (SFEI) Grassland Bypass Project Report October 2001 December Richmond, CA. San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Narrative and Graphical Summary, January 2010 to December Richmond, CA. U.S. Bureau of Reclamation et al Compliance Monitoring Program for the Use and Operation of the Grassland Bypass Project, September U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, CA. U.S. Bureau of Reclamation Grassland Bypass Project Annual Report. October 1, 1996 through September 30, U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, CA. U.S. Bureau of Reclamation et al. June Monitoring Program for the Operation of the Grass land Bypass Project, Phase II. Sacramento, CA. U.S. Bureau of Reclamation, et. al. August 22, Quality Assurance Project Plan for the Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project. Sacramento, CA. Tables Table 1a, b, c. Summary of Water Quality Monitoring Plan Table 2. Summary of Selenium Water Quality Objectives Table 3a, b, c. Selenium Concentrations in the Grasslands Watershed and San Joaquin River Table 4a, b, c. Boron Concentrations in the Grassland Watershed and San Joaquin River Table 5a, b, c. Molybdenum Concentrations in the Grasslands Watershed and San Joaquin River Table 6. Nutrient Series Data for Station B Table 7. Nutrient Series Data for Station C Table 8. Nutrient Series Data for Station D Table 9. Nutrient Series Data for Station G Table 10. Nutrient Series Data for Station N Figures Figure 1. Selenium Concentration in the San Joaquin River Figure 2. Monthly Mean Selenium Concentration in the San Joaquin River at Crows Landing Figure 3. Mean Monthly Selenium Concentration in the Grassland Wetland Supply Channels Figure 4. Weekly Grab Selenium Concentration in Mud Slough (North) below Sand Luis Drain (Station D) Figure 5. Weekly Grab Selenium Concentration in Mud Slough (North) above San Luis Drain (Station C)

68 66 GRASSLAND BYPASS PROJECT TABLE 1. SUMMARY OF WATER QUALITY MONITORING PLAN LOCATION SITE DESCRIPTION PURPOSE San Luis Drain A inflow to SLD water quality of inflow B discharge from SLD water quality of discharge (for Se load calculation) ANALYTICAL PARAMETER Se, B, SC FREQUENCY weekly composite SAMPLING METHODOLOGY auto-sampler SC, TSS weekly mid-channel, grab Se, B, SC ph, SC, Temp, Se, B, TSS1, Mo2, Nutrients3 daily composite weekly auto-sampler mid-channel, grab C upstream of SLD discharge Mud Slough (north) base water quality prio vvr to receiving drainage discharges ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab Mud Slough (north) D downstream of discharge Mud Slough (north) water quality as impacted by drainage discharge ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly mid-channel, grab I/I2 back water water quality impact of Mud Slough (north) flooding in Kesterson Refuge Se, B, SC annually grab F Salt Slough water quality of habitat and to track improvements in former drainage conveyance channel ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab J Camp 13 verify no discharge of drainage provision, water quality of wetland water supply channel Se, B, SC weekly grab Wetland Channels K Agatha Canal verify no discharge of drainage provision, water quality of wetland water supply channel Se, B, SC weekly grab L2 San Luis Canal water quality of wetland water supply channel Se, B, SC weekly grab M2 Santa Fe Canal water quality of wetland water supply channel Se, B, SC weekly grab G at Fremont Ford (upstream of drainage inflow) track improvements in former drainage conveyance channel and characterize water quality of habitat ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab San Joaquin River N at Crows Landing (downstream of Merced River confluence) characterize water quality of habitat Se, B, SC ph, SC, Temp, Se, B, Mo2, Nutrients3 daily composite weekly auto-sampler grab R at China Island water quality downstream of Mud Slough discharge ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab Notes: 1 TSS required daily during storm events 2 Molybdenum required monthly 3 Nutrients required monthly September through February and every other week March through August

69 CHAPTER 4: WATER QUALITY MONITORING 67 TABLE 1b. COMPARISON OF CHANGES IN THE 2013 WATER QUALITY MONITORING PLAN REVISION 2005 MRP 2013 REVISED MP LOCATION SITE DESCRIPTION PURPOSE ANALYTICAL PARAMETER FREQUENCY SAMPLING METHODOLOGY ANALYTICAL PARAMETER FREQUENCY SAMPLING METHODOLOGY A inflow to SLD water quality of inflow Se, B, SC weekly composite auto-sampler Selenium daily mid-channel, grab SC, TSS weekly mid-channel, grab TSS weekly mid-channel, grab Se, B, SC daily composite auto-sampler Boron, Selenium, Specific conductance daily composite auto-sampler B discharge from SLD water quality of discharge (for Se load calculation) General minerals, total metals, nutrients Dissolved selenium, selenium in particulates, toxicity monthly mid-channel, grab quarterly mid-channel, grab San Luis Drain Dissolved metals, bacteria, pesticides biannual mid-channel, grab ph, SC, Temp, Se, B, TSS1, Mo2, Nutrients3 weekly mid-channel, grab Physicals, TSS weekly mid-channel, grab C upstream of SLD discharge Mud Slough (north) base water quality prior to receiving drainage discharges ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab D downstream of discharge Mud Slough (north) water quality as impacted by drainage discharge ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly mid-channel, grab Physicals, Selenium weekly mid-channel, grab General minerals, total metals, nutrients Dissolved selenium, selenium in particulates, toxicity monthly mid-channel, grab quarterly mid-channel, grab Mud Slough (north) Dissolved metals, bacteria, pesticides biannual mid-channel, grab I/I2 back water water quality impact of Mud Slough (north) flooding in Kesterson Refuge Se, B, SC annually grab Physicals, Selenium weekly mid-channel, grab

70 68 GRASSLAND BYPASS PROJECT TABLE 1b. COMPARISON OF CHANGES IN THE 2013 WATER QUALITY MONITORING PLAN REVISION (CONTIN.) 2005 MRP 2013 REVISED MP LOCATION SITE DESCRIPTION PURPOSE ANALYTICAL PARAMETER FREQUENCY SAMPLING METHODOLOGY ANALYTICAL PARAMETER FREQUENCY SAMPLING METHODOLOGY F Salt Slough J Camp 13 water quality of habitat and to track improvements in former drainage conveyance channel verify no discharge of drainage provision, water quality of wetland water supply channel ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab Physicals, Selenium weekly mid-channel, grab Se, B, SC weekly grab General minerals, total metals, nutrients Dissolved selenium, selenium in particulates, toxicity Dissolved metals, bacteria, pesticides Se, physicals, when water is flowing monthly mid-channel, grab quarterly mid-channel, grab biannual mid-channel, grab weekly grab Wetland Channels K Agatha Canal verify no discharge of drainage provision, water quality of wetland water supply channel Se, B, SC weekly grab Se, physicals, when water is flowing weekly grab L2 San Luis Canal M2 Santa Fe Canal H at Hills Ferry water quality of wetland water supply channel water quality of wetland water supply channel water quality of San Joaquin River prior to Merced River confluence Se, B, SC weekly grab Se, B, SC weekly grab Se,SC, Flow. Temp weekly real time/grab SC, Flow. Temp weekly real time/grab N R at China Island G at Fremont Ford (upstream of drainage inflow) at Crows Landing (downstream of Merced River confluence) water quality of San Joaquin River prior to Merced River confluence track improvements in former drainage conveyance channel and characterize water quality of habitat characterize water quality of habitat Se, B, SC Se weekly grab Se weekly grab ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab daily composite auto-sampler Selenium, Specific conductance daily composite auto-sampler San Joaquin River Notes: 1 TSS required daily during storm events 2 Molybdenum required monthly 3 Nutrients required monthly September through February and every other week March through August ph, SC, Temp, Se, B, Mo2, Nutrients3 weekly grab Physicals, Boron weekly grab

71 CHAPTER 4: WATER QUALITY MONITORING 69 TABLE 1c. SUMMARY OF THE PROPOSED 2013 REVISED MONITORING PROGRAM FREQUENCY STATIONS PARAMETERS MEDIA AGENCY NOTES Real-time D, F, H, N Flow, specific conductivity, temperature W USGS preliminary data on CDEC J*, K* Flow, specific conductivity, temperature W Grasslands WD Daily A, B2 Flow, specific conductivity, temperature W Panoche DD A Selenium (total) W Panoche DD grab B3, N Selenium (total), boron W MP-157 autosamplers Weekly B3, D, F, R, I2** Physicals W SCCAO B3, D, F, R, J*, K*, I2** Selenium (total) W SCCAO B3, D, F, R General minerals W SCCAO Monthly B3, D, F, R Metals (total) W SCCAO A, B3 Total suspended solids W Panoche DD B3, D, F, R Nutrients W SCCAO B3, D, F, R Three-species chronic toxicity W Contractor Quarterly (March, June, September, November) D, F, R, I2** Biological B Contractor B3, D, F, R, I2** Particulate selenium W SCCAO B3, D, F, R, I2** Selenium (dissolved) W SCCAO B3, D, F, R Metals (dissolved) W MP-157 Biannual (March, September) B3, D, F, R Pesticides W SCCAO B3, D, F, R Bacteria W SCCAO B3, D, F, R, I2 Sediment toxicity S MP-157 Seasonal (April- June) Annual I2** Sediment S SCCAO San Luis Drain Accumulation of sediment S Panoche DD SLD, D, F, R, I2** Sediment mercury, selenium, TOC, pesticides,etc S MP-157 * = samples will be collected when water is passing site SCCAO - Reclamation. Fresno Office ** = samples will be collected when this site is floodedmp Reclamation Sacramento Office 1/14/13 B - biota fish, invertebrates S - sediment W - water Distances Miles Site A to Site B Site B3 to B 0.7 Site B to B2 terminus 1.9 SJR Mud Slough to China Island 1.3 China Island to Merced River 1.8

72 70 GRASSLAND BYPASS PROJECT TABLE 2. SUMMARY OF SELENIUM WATER QUALITY OBJECTIVES AND COMPLIANCE TIME SCHEDULE [Selenium Water Quality Objectives (in bold) and Performance Goals (in italics)] Water Body/Water Year 31 December 31 December Type Mud Slough (north) and the San Joaquin River from the Mud Slough confluence to the Merced River 15 ug/l monthly mean 5 ug/l 4-day average 1 The water year classification will be established using the best available estimate of the San Joaquin Valley water year hydrologic classification (as defined in Footnote17 for Table 3 in the State Water Resources Control Board's Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary, May 1995) at the 75% exceedance level using data from the Department of Water Resources Bulletin 120 series. The previous water year's classification will apply until an estimate is made of the current wateryear. TABLE 3a. SELENIUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2012 STATION ID DESCRIPTION JAN-12 FEB- 12 MAR- 12 APR- 12 MEAN MONTHLY CONCENTRATION (ΜG/L) MAY- 12 JUN- 12 JUL- 12 AUG- 12 SEP- 12 OCT- 12 NOV- 12 DEC- 12 WQO C D Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge F Salt Slough at Lander Avenue NA G SJR at Fremont Ford N SJR at Crows Landing Daily Autosamples Notes: Bold = water quality objective exceedance WQO = water quality objective in µg/l NA = no data available TABLE 3b. SELENIUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2013 STATION ID C D F DESCRIPTION Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge Salt Slough at Lander Avenue JAN- 13 FEB- 13 MAR- 13 APR- 13 MEAN MONTHLY CONCENTRATION (ΜG/L) MAY- 13 JUN- 13 JUL NA NA NA AUG- 13 SEP- 13 OCT- 13 NOV- 13 DEC- 13 WQO G SJR at Fremont Ford NA NA NA 2.0 N SJR at Crows Landing Daily Autosamples NA Notes: Bold = water quality objective exceedance WQO = water quality objective in µg/l NA = no data available

73 CHAPTER 4: WATER QUALITY MONITORING 71 TABLE 3c. SELENIUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2014 STATION ID C D F G DESCRIPTION Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge Salt Slough at Lander Avenue SJR at Fremont Ford JAN- 14 FEB- 14 MAR- 14 APR- 14 MEAN MONTHLY CONCENTRATION (ΜG/L) MAY- JUN- JUL- AUG- SEP NA NA NA NA NA NA NA N SJR at Crows Landing Daily Autosamples Notes: Bold = water quality objective exceedance WQO = water quality objective in µg/l NA = no data available OCT- 14 NOV- 14 DEC- 14 WQO TABLE 4a. BORON CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2012 STATION ID C D F G N Notes: DESCRIPTION Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge Salt Slough at Lander Avenue SJR at Fremont Ford SJR at Crows Landing Daily Autosamples JAN- 12 FEB- 12 MAR- 12 APR- 12 MEAN MONTHLY CONCENTRATION (MG/L) MAY- 12 JUN- 12 JUL- 12 AUG- 12 SEP- 12 OCT- 12 NOV- 12 DEC- 12 MONTHLY WQO* a a a a a 2.0 a a a a a 2.0 a a a a a 2.0 a a a a a /1.0** Bold = water quality objective exceedance a = objective only applies 15 March through 15 September WQO = water quality objective in mg/l NA = no data available * =Table III-1, The Water Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board Central Valley Region 4th edition ** 0.8 mg/l 15 March- 15 September; 1.0 mg/l 16 September- 14 March

74 72 GRASSLAND BYPASS PROJECT TABLE 4b. BORON CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2013 STATION ID DESCRIPTION JAN- 13 FEB- 13 MAR- 13 APR- 13 MAY- 13 MEAN MONTHLY CONCENTRATION (MG/L) JUN- 13 JUL- 13 AUG- 13 SEP- 13 OCT- 13 NOV- 13 DEC- 13 MONTHLY WQO* C Mud Slough (N) upstream of SLD Discharge a a a a a 2.0 D Mud Slough (N) downstream of SLD Discharge a a a a a 2.0 F Salt Slough at Lander Avenue a a a a a 2.0 G SJR at Fremont Ford a a a a a 2.0 N SJR at Crows Landing Daily Autosamples Notes: Bold = water quality objective exceedance a = objective only applies 15 March through 15 September WQO = water quality objective in mg/l NA = no data available *=Table III-1, The Water Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board Central Valley Region 4th edition TABLE 4c. BORON CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2014 STATION ID DESCRIPTION JAN- 14 FEB- 14 MAR- 14 APR- 14 MAY- 14 MEAN MONTHLY CONCENTRATION (MG/L) JUN- 14 JUL- 14 AUG- 14 SEP- 14 OCT- 14 NOV- 14 DEC- 14 MONTHLY WQO* C Mud Slough (N) upstream of SLD Discharge a a a a a 2.0 D F Mud Slough (N) downstream of SLD Discharge Salt Slough at Lander Avenue a a a a a 2.0 a a a a a 2.0 G SJR at Fremont Ford a a a a a 2.0 N SJR at Crows Landing Daily Autosamples Notes: Bold = water quality objective exceedance a = objective only applies 15 March through 15 September WQO = water quality objective in mg/l NA * = no data available =Table III-1, The Water Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board Central Valley Region 4th edition

75 CHAPTER 4: WATER QUALITY MONITORING 73 TABLE 5a. MOLYBDENUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2012 STATION ID C D DESCRIPTION Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge JAN- 12 FEB- 12 MAR- 12 APR- 12 MAY- 12 MONTHLY CONCENTRATION (UG/L) JUN- 12 JUL- 12 AUG- 12 SEP- 12 OCT- 12 NOV- 12 DEC- 12 MONTHLY WQO F G N Salt Slough at Lander Avenue SJR at Fremont Ford SJR at Crows Landing Grab Samples Notes: Bold = water quality objective exceedance WQO = water quality objective in ug/l na = no data available na TABLE 5b. MOLYBDENUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2013 STATION ID C D F G N DESCRIPTION Mud Slough (N) upstream of SLD Discharge Mud Slough (N) downstream of SLD Discharge Salt Slough at Lander Avenue SJR at Fremont Ford SJR at Crows Landing Grab Samples JAN- 13 FEB- 13 MAR- 13 APR- 13 MAY- 13 MONTHLY CONCENTRATION (UG/L) JUN- JUL- AUG- SEP OCT- 13 NOV- 13 DEC- 13 MONTHLY WQO NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.0 Notes: Bold = water quality objective exceedance WQO = water quality objective in ug/l na = no data available

76 74 GRASSLAND BYPASS PROJECT TABLE 5c. MOLYBDENUM CONCENTRATIONS IN THE GRASSLAND WATERSHED AND SAN JOAQUIN RIVER: 2014 STATION ID DESCRIPTION JAN- 14 FEB- 14 MAR- 14 APR- 14 MAY- 14 MONTHLY CONCENTRATION (UG/L) C Mud Slough (N) upstream of SLD NA NA NA NA NA NA NA 25.0 NA Discharge D Mud Slough (N) downstream of NA NA SLD Discharge F Salt Slough at Lander Avenue NA NA G SJR at Fremont Ford NA NA NA NA N SJR at Crows Landing Grab NA NA NA 5.6 NA NA NA 10.0 Samples Notes: Bold = water quality objective exceedance WQO = water quality objective in ug/l na = no data available JUN- 14 JUL- 14 AUG- 14 SEP- 14 OCT- 14 NOV- 14 DEC- 14 MONTHLY WQO TABLE 6. NUTRIENT SERIES DATA, SITE B, SAN LUIS DRAIN NEAR TERMINUS PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 05 Jan T 0.07 < T T Feb V < V Mar < T Mar < Apr Apr Tvv T May T, V 0.10 < May T Jun T L Jun V Jul L U, L Jul < Aug T Aug V T 0.40 L Aug T 0.12 V < Sep Oct V L, V Nov 2012 < < L Dec T Jan T T Feb Mar < Mar T Apr L V < L Apr < May T,U 0.14 T,V T,L,U May L V < V 0.59 V,L,U May <

77 CHAPTER 4: WATER QUALITY MONITORING 75 TABLE 6. NUTRIENT SERIES DATA, SITE B, SAN LUIS DRAIN NEAR TERMINUS (CONT.) PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 18 Jun < Jul U 0.28 U < V 0.68 L Jul T Jul V L Aug < Aug 2013 < V,U Sep 2013 < T.13 T < Mar 2014 < T < May T < Jun < U Jul 2014 < < V Sep 2014 < T < T Oct 2014 < U 0.35 U < 2.0 < Dec Data Source: Notes: Bureau of Reclamation, Mid-Pacific Region B NA H L V T U Water quality objective exceedance of 10 mg/l Ammonia Toxicity Threshold Exceedance No sample collected, result not available Result may have high bias Result may have low bias Result may vary excessively Result obtained past holding time Result determined to be outlier at the time of data validation

78 76 GRASSLAND BYPASS PROJECT TABLE 7. NUTRIENT SERIES DATA, SITE C, MUD SLOUGH (NORTH) UPSTREAM OF SLD PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 05 Jan T T T Feb V V Mar T Mar Apr Apr T T May T, V May T Jun T L Jun V Jul 2012 < L L Jul Aug T Aug V T 0.10 L Aug T 0.12 V Sep Si Oct V L, V Nov L Dec T Jan T T Feb H Mar Mar T Apr L V L Apr May T 0.30 T, V T, L May L V 0.21 V 0.11 V, L May < Jun Jul U H, V 0.18 L Jul T Jul V L Aug Aug V Sep T 0.32 T Mar U 0.69 T, U Oct 2014 < < 1.0 < Dec U 4.73 Data Source: Notes: Bureau of Reclamation, Mid-Pacific Region Water quality objective exceedance of 10 mg/l B Ammonia Toxicity Threshold Exceedance NA No sample collected, result not available H Result may have high bias L Result may have low bias V Result may vary excessively T Result obtained past holding time U Result determined to be outlier at the time of data validation

79 CHAPTER 4: WATER QUALITY MONITORING 77 TABLE 8. NUTRIENT SERIES DATA, SITE D, MUD SLOUGH (NORTH) DOWNSTREAM OF SLD PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 05 Jan L,T T T Feb V V Mar T Mar < Apr Apr T 0.43 < T May T, V May T Jun T L Jun U V Jul < U,L Jul L Aug < Aug T L, V T 0.15 L Aug V < Sep T 0.12 < Oct V L, V Nov U 0.18 L Dec T Jan T T Feb H Mar Mar T L Apr L V L Apr < May T 0.25 T, V T, L, U May L V V 0.32 V, L May U < Jun Jul < V 0.31 L Jul T Jul V < L Aug U 0.16 < Aug V Sep T 0.29 T Nov Dec Jan V T Feb T T L Mar T, U May T < Jun U 3.5 U 0.18 < U Jul 2014 < L U 0.13 < V Sep 2014 < T < T Oct 2014 < < 1.0 < Dec U 0.53 U 4.73 Data Source: Notes: Bureau of Reclamation, Mid-Pacific Region Water quality objective exceedance of 10 mg/l B NA H L V T U Ammonia Toxicity Threshold Exceedance No sample collected, result not available Result may have high bias Result may have low bias Result may vary excessively Result obtained past holding time Result determined to be outlier at the time of data validation

80 78 GRASSLAND BYPASS PROJECT TABLE 9. NUTRIENT SERIES DATA, SITE G, SAN JOAQUIN RIVER AT FREMONT FORD PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 05 Jan T T < T Feb V V Mar T Mar Apr Apr T T May T, V May T Jun T L Jun V < Jul L L Jul Aug T Aug V 0.21 T 0.95 L, U Aug T 0.20 V Sep Oct V L, V Nov L Dec T Jan Feb H Mar Mar Apr V V 0.15 V L Apr May T, V 1.2 T 0.20 T, V 0.20 T, V 0.15 T, L May V, U V, U 0.58 V, U V, L May < Jun Jul L Jul Jul < L Aug Aug Sep T 1.1 T 0.18 T 0.18 T Mar T T 0.24 T < May T T 0.16 T Jun < Jul V Sep T T 0.29 T Dec Data Source: Notes: California Regional Water Quality Control Board, Central Valley Region Bureau of Reclamation, Mid-Pacific Region Water quality objective exceedance of 10 mg/l B Ammonia Toxicity Threshold Exceedance NA H L V T U No sample collected, result not available Result may have high bias Result may have low bias Result may vary excessively Result obtained past holding time Result determined to be outlier at the time of data validation

81 CHAPTER 4: WATER QUALITY MONITORING 79 TABLE 10. NUTRIENT SERIES DATA, SITE N, SAN JOAQUIN RIVER AT CROWS LANDING PARAMETER UNITS NITRATE MG/L AS N TOTAL KJELDHAL NITROGEN MG/L TOTAL PHOSPHORUS MG/L ORTHO PHOSPHATE MG/L AS P DISSOLVED AMMONIA MG/L AS N AMMONIA TOXICITY THRESHOLD MG/L AS N 05 Jan T T < T Feb V V Mar T Mar Apr Apr T T May T, V May T Jun T L Jun V < Jul L L Jul Aug T Aug V 0.14 T 0.18 L Aug T 0.13 V Sep Oct V L, V Nov < L Dec T Jan T T Feb H Mar Mar T Apr L V L Apr May T 0.20 T, V T, L May L V V V, L May < Jun Jul H, V L Jul T Jul V < L Aug Aug V Sep T T May T 0.02 < Jun < 0.05 < Jul V Sep U T 0.20 T Data Source: Notes: Bureau of Reclamation, Mid-Pacific Region Water quality objective exceedance of 10 mg/l B Ammonia Toxicity Threshold Exceedance NA No sample collected, result not available H Result may have high bias L Result may have low bias V Result may vary excessively T Result obtained past holding time U Result determined to be outlier at the time of data validation

82 80 GRASSLAND BYPASS PROJECT FIGURE 1. SELENIUM CONCENTRATION IN THE SAN JOAQUIN RIVER Figure 1. Selenium Concentration in the San Joaquin River SJR at Fremont Ford (weekly grab) 3.0 SJR at Crows Landing (4-day running average) SJR at Crows Landing (weekly grab) 2.5 Selenium concentration (ug/l) Jan-12 Mar-12 May-12 Jul-12 Sep-12 Nov-12 Jan-13 Mar-13 May-13 Jul-13 Sep-13 Nov-13 Jan-14 Mar-14 May-14 Jul-14 Sep-14 Nov-14 FIGURE 2. MONTHLY MEAN SELENIUM CONCENTRATION IN THE SAN JOAQUIN RIVER AT CROWS LANDING (SITE N) Selenium ( g/l) Jan-12 Mar-12 May-12 Jul-12 Sep-12 Nov-12 Jan-13 Mar-13 May-13 Jul-13 Sep-13 Nov-13 Jan-14 Mar-14 May-14 Jul-14 5 g/l objective Sep-14 Nov-14

83 CHAPTER 4: WATER QUALITY MONITORING 81 4 FIGURE 3. MEAN MONTHLY SELENIUM CONCENTRATION IN THE GRASSLAND WETLAND SUPPLY CHANNELS Site F Salt Slough Site J Camp 13 Ditch Site K Agatha Canal Site L2 San Luis Canal Site M2 Santa Fe Canal Monthly Mean Objective (2ug/L) Selenium ( g/l) Jan-12 Mar-12 May-12 Jul-12 Sep-12 Nov-12 Jan-13 Mar-13 May-13 Jul-13 Sep-13 Nov-13 Jan-14 Mar-14 May-14 Jul-14 Sep-14 Nov-14 FIGURE 4. WEEKLY GRAB SELENIUM CONCENTRATION IN MUD SLOUGH (NORTH) BELOW SAN LUIS DRAIN (SITE D) Se ( g/l) 2015 Objective (4-day running average) 2019 Objective (4-day running average) Selenium ( g/l) Jan-12 Mar-12 May-12 Jul-12 Sep-12 Nov-12 Jan-13 Mar-13 May-13 Jul-13 Sep-13 Nov-13 Jan-14 Mar-14 May-14 Jul-14 Sep-14 Nov-14

84 82 GRASSLAND BYPASS PROJECT FIGURE 5. WEEKLY GRAB SELENIUM CONCENTRATION IN MUD SLOUGH (NORTH) ABOVE SAN LUIS DRAIN (SITE C) Se ( g/l) Selenium Objective(monthly average) 4 Selenium ( g/l) Jan-12 Mar-12 May-12 Jul-12 Sep-12 Nov-12 Jan-13 Mar-13 May-13 Jul-13 Sep-13 Nov-13 Jan-14 Mar-14 May-14 Jul-14 Sep-14 Nov-14

85 05 FLOW, CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 83 SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN Michael C. S. Eacock1 Nigel W.T. Quinn 2 Jeffrey E. Papendick3 1 Natural Resource Specialist, US Bureau of Reclamation, South-Central California Area Office, 1243 N Street, Fresno, California meacock@usbr.gov 2 Staff Geological Scientist/Water Resources Engineer, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Building 70A-3317H, Berkeley, California nquinn@lbl.gov 3 Natural Resources Technician, US Bureau of Reclamation, South-Central California Area Office, 1243 N Street, Fresno, California jpapendick@usbr.gov SUMMARY This chapter includes tables of data which summarize monthly flows, salt loads, and selenium loads that passed stations A and B2 between 2012 and the end of 2014 and for the entire eighteen years of the Project (Figure 1). Although the 28-mile reach utilized by the Grassland Bypass Project is lined with concrete, water continued to enter the San Luis Drain between stations A and B2 during the winter months when wetlands beside the drain were flooded. There was an increase in flow between the stations during 26 of the 36 months between January 2012 and December The greatest increase occurred in October 2014 when there was an 80 percent increase in flow between the stations (Table 1a). For most of the three year span, there was a corresponding increase in salt load between the stations as well. The greatest increase occurred in October 2014 when there was an 86 percent increase in salt load between the stations (Table 2a). Table 3a lists monthly gains and losses of selenium between the stations between January 2012 and December Selenium loads increased during 13 of the 36 months, with a maximum increase of 88 percent occurring in October However, the monthly loads decreased during the remaining 23 months; a maximum decrease of 105 percent occurred during April The difference in selenium between the stations may be due to measurement error, microbial uptake, adsorption to sediments, volatilization, or seepage of seleniferous water into or out of the drain between stations A and B2. Table 4a lists the monthly effects of rainfall and evapotranspiration on the volume of water in the San Luis Drain during 2012 and Column 9 in this table lists the monthly change in flow between the station that is not the result of rainfall upon, and evaporation from, the water surface of the drain. These calculations suggest that the seasonal increases in flow in the drain are due to seepage from adjacent wetlands. Table 5a summarizes the differences in flow, salt load, selenium load, and volume between stations A and B2 between January 2012 and December Table 5b summarizes the maximum and minimum differences in flow, salt loads, and selenium loads during the entire seventeen years of the Grassland Bypass Project. BACKGROUND Seepage into the San Luis Drain most likely occurs through cracks and one-way weep valves that equalize hydraulic pressure to prevent the concrete lining from buckling. Along the drain, the water surface elevation of adjacent wetlands, when flooded in the fall and winter, is often higher than the elevation of water in the drain. Leakage from the drain can occur where the concrete lining is fractured or between adjacent concrete panels. Other losses from the drain include direct evaporation of water and evapotranspiration by algae and aquatic plants.

86 84 GRASSLAND BYPASS PROJECT FLOW DIFFERENCES BETWEEN STATIONS A AND B2 Table 1a compares the monthly flows of water that passed stations A and B2. Note the increases in flow during the autumn and winter months when adjacent wetlands are flooded. Tables 1b and 1c summarize the difference in the annual amounts of water that flowed past stations A and B2 during the entire Project. The difference in monthly flows between the stations for 2012 through 2014 ranged from a loss of 80 to a gain of 500 acre-feet (Table 1a). The largest increases typically occurred between September and March when wetlands beside the drain were flooded. There was a net annual increase in flow of 18 percent during WY 2012, 20 percent during WY 2013, and 33 percent in WY 2014 (Table 1b). In previous years, we thought that monthly differences in flows were partly the result of cumulative errors from different analytical methods and equipment. Beginning in October 2005, flow at station B2 is measured the same way as at station A using a sharp-crested weir with a precision of ± 5 percent. The pattern of seasonal increases in flow has continued with the comparable measurements of flow. In Table 4a, we calculate the net water gain or loss each month by taking into account precipitation upon, and evapotranspiration from, the water surface in the drain. Once precipitation and evapotranspiration are accounted for, the difference in flow between stations A and B2 from January 2012 through December 2014 ranges from a loss of 38 percent to a gain of 59 percent. The autumn and winter months (September - March) show large increases in flow. The maximum percent flow difference between stations A and B occurred in October 2012, with a value of 64%. SALT MASS BALANCE BETWEEN STATIONS A AND B Table 2a lists the monthly loads of salt in water that passed stations A and B2. Figures 4abc shows the monthly loads of salt in water that passed stations A and B2. The change in salt loads between the stations ranged from a loss of 1,030 tons to a gain of 1,940 tons. As with the observed changes in flows, the increases in salt occurred during autumn and winter months when the adjacent wetlands were flooded. In WY 2012, the annual loads of salt decreased by about thirteen percent followed by a 19 percent increase in WY 2013 and a 24 percent increase in WY 2014 (Table 2b). Since salinity is a conservative chemical constituent, the monthly salt load measured at station A should be identical to that at station B2. An increase in salt load implies an inflow of saline water into the drain if other factors such as precipitation and evaporation are taken into account. A decrease in salt load would imply the loss of saline water from the drain, or inflow of less saline water. In previous years, we thought that monthly differences in salt loads were the result of cumulative errors from the use of different analytical methods and equipment. Equipment drift in the electrical conductivity (EC) sensor response can affect the computation of salt load. However, EC is measured with identical sensors and methods at both stations. USGS staff considers the EC sensor at station B2 to be accurate within three percent. In previous years, algae bio-fouling of the probe at station B caused errors of more than 30 percent during summer months, but diligent maintenance prevented this from occurring and kept the rate of error to less than ten percent. Over the past three years the flow weighted EC was lower at station B2 than station A for 20 of the 36 months as listed in Table 2a. A maximum salt gain of 86% between stations A and B occurred during October 2014, the maximum salt loss of -36% occurred in April SELENIUM MASS BALANCE BETWEEN STATIONS A AND B A simple mass balance of selenium was calculated to improve understanding of selenium mass transport and mass transfer dynamics within the San Luis Drain. Selenium is a non-conservative chemical constituent. The data are presented in Tables 3a, 3b, and 3c. Figures 5abc shows the monthly loads of selenium at both stations during 2012, 2013, and The differences in selenium loads along the San Luis Drain ranged from a loss of 23 pounds (May 2012) to a gain of 16 pounds (February 2013 and March 2014). The maximum selenium load gain between stations A and B was 88% in October 2014, the maximum loss occurred in April 2013 with a value of -105%.

87 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 85 DISCUSSION Table 5a is a summary of monthly differences in flow, salinity, and selenium between stations A and B2. The monthly differences in selenium loads did not correspond to differences in flows and salt loads between the stations. For example, during October 2012, there was a 64 percent increase in flow, 49 percent increase in salt loads, and a 12 percent increase in selenium load. The monthly differences in selenium loads may be caused by the different frequencies at which water quality samples are collected at each station. Flow data, when combined with continuous and discrete selenium data, are used to compute this mass balance. Prior to 2010, selenium sampling did not occur at the same frequency at both stations A and B2. Selenium samples were collected by auto-samplers at both stations. At station B2, several samples were collected each day; the composite of each day s samples were analyzed in the laboratory. At station A, seven daily samples were mixed to produce a single weekly composite for analysis by the laboratory. Panoche Water District has been measuring selenium in the daily samples collected at station A since May CONCLUSIONS In the past three years of the Grassland Bypass Project, flow of water in the San Luis Drain increased during autumn and winter months when adjacent wetlands were flooded. The monthly increases in flow (Table 1a) did not correspond with local rainfall or evapotranspiration (Table 4a). The annual changes in flows have ranged from a loss of one percent to a gain of twenty percent (Table 1b). The monthly loads of salt have varied during from a loss of 1,030 tons to a gain of 1, 940 tons, with gains typically occurring between September and February while adjacent wetlands have been flooded (Table 2a). The net annual change in salt loads ranged from a loss of 13 percent to a gain of 24 percent (Table 2b). The monthly loads of selenium varied from a loss of 23 pounds to a gain of 16 pounds during (Table 3a). These differences do not correspond to the observed gain of flows during the autumn and early winter. The method for measuring selenium at both stations has been the same since May The differences in selenium loads, likely due to natural processes, cannot be determined under the current monitoring program. TABLES Tables 1a,b,c. Comparison of Flow Measurements in the San Luis Drain Tables 2a,b,c. Comparison of Salinity and Salt Loads in the San Luis Drain Tables 3a,b,c. Comparison of Selenium Measurements in the San Luis Drain Tables 4a,b,c. Gain or Loss due to Precipitation and Evapotranspiration Tables 5a,b. Mass Balance in the San Luis Drain FIGURES Figure 1. Map of the Grassland Bypass Project Figure 2. Grassland Bypass Project - Schematic Diagram Showing Locations of GBP Monitoring Stations Relative to Major Hydrologic Features of the Study Area Figure 3a,b,c. Comparison of Flows in the San Luis Drain Figure 4a,b,c. Comparison of Salt Loads in the San Luis Drain Figure 5a.b.c. Comparison of Selenium Loads in the San Luis Drain

88 86 GRASSLAND BYPASS PROJECT TABLE 1a. COMPARISON OF FLOW MEASUREMENTS IN THE SAN LUIS DRAIN MONTHLY AVERAGE FLOW STATION A CFS STATION B CFS TOTAL FLOW STATION A ACRE-FEET/ MONTH STATION B ACRE-FEET/ MONTH DIFFERENCE ACRE-FEET/ MONTH DIFFERENCE AS PERCENT OF STATION B January % February , % March ,240 1, % April % May % June % July % August % September % October % November % December , % January , % February , % March % April % May % June % July % August % September % October % November % December % January % February ,040 1, % March % April % May % June % July % August % September % October % November % December ,450 2, % Data sources: Station A - San Luis & Delta-Mendota Water Authority Station B2 - San Luis & Delta-Mendota Water Authority Rainfall measured at Panoche WD

89 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 87 TABLE 1b. COMPARISON OF FLOW MEASUREMENTS, WATER YEARS MONTHLY AVERAGE FLOW STATION A CFS STATION B CFS TOTAL FLOW STATION A ACRE-FEET STATION B ACRE-FEET DIFFERENCE DIFFERENCE AS PERCENT OF STATION B WY ,800 37, % WY ,570 45,950 2,380 5% WY ,510 32,310 1,800 6% WY ,330 31,260 1,930 6% WY ,050 28,250 1,200 4% WY ,820 28,400 2,580 9% WY ,250 27,270 2,020 7% WY ,370 27,700 2,330 8% WY ,540 30,160 2,620 9% WY ,080 25,970 2,890 11% WY ,480 18,540 2,060 11% WY ,230 15,670 2,440 16% WY ,340 13, % WY ,610 14, % WY ,540 18,510 1,970 11% WY ,620 10,490 1,870 18% WY ,010 10,040 2,030 20% WY ,820 7,150 2,330 33% TABLE 1c. COMPARISON OF FLOW MEASUREMENTS, CALENDAR YEARS MONTHLY AVERAGE FLOW STATION A CFS STATION B CFS TOTAL FLOW STATION A ACRE-FEET STATION B ACRE-FEET DIFFERENCE DIFFERENCE AS PERCENT OF STATION B ,590 37, % ,220 46,240 2,020 4% ,910 32,250 2,340 7% ,920 30,210 1,290 4% ,190 28,010 1,820 6% ,520 28,460 1,940 7% ,360 27,550 2,190 8% ,730 28,290 2,560 9% ,870 29,610 2,740 9% ,180 25,890 2,710 10% ,760 17,990 2,230 12% ,880 15,860 1,980 12% ,340 12, % ,850 14, % ,650 18,020 2,370 13% ,910 10,020 2,110 21% ,750 9,710 1,960 20% ,640 8,370 1,730 21%

90 88 GRASSLAND BYPASS PROJECT TABLE 2a. COMPARISON OF SALINITY AND SALT LOADS IN THE SAN LUIS DRAIN FLOW-WEIGHTED ELECTRICAL CONDUCTIVITY STATION A ΜS/CM STATION B ΜS/CM SALT LOADS STATION A TONS PER MONTH STATION B TONS PER MONTH DIFFERENCE DIFFERENCE AS PERCENT OF STATION B January ,040 2,672 2,940 2, % February ,489 2,838 2,910 3, % March ,910 3,663 6,120 5, % April ,739 4,368 3,930 2,900-1,030-36% May ,605 4,774 3,340 3, % June ,106 4,782 3,600 3, % July ,233 4,936 4,530 3, % August ,857 4,975 2,690 2, % September ,721 4,657 1,090 1, % October ,743 3,422 1,150 2,270 1,120 49% November ,553 3,454 1,790 3,100 1,310 42% December ,124 3,994 3,710 4, % January ,323 4,575 4,130 5,300 1,170 22% February ,878 4,719 4,030 5,030 1,000 20% March ,757 4,846 4,160 4, % April ,114 5,985 4,320 4, % May ,571 5,964 3,360 4, % June ,961 6,445 3,040 3, % July ,388 6,614 5,270 5, % August ,743 7,500 5,230 6, % September ,475 8,772 3,230 5,120 1,890 37% October ,335 6,335 3,440 4,980 1,540 31% November ,761 5,078 2,650 3,780 1,130 30% December ,673 5,501 2,970 4,150 1,180 28% January ,092 5,442 4,640 5, % February ,628 6,105 6,930 7, % March ,613 5,978 3,990 5,410 1,420 26% April ,753 6,636 2,860 3, % May ,938 6,754 1,670 2,790 1,120 40% June ,892 7,796 2,980 3, % July ,471 9,705 2,110 3,420 1,310 38% August ,910 10, % September ,697 13, % October ,300 15, % November ,340 9,005 4,680 5, % December ,310 6,127 15,560 17,500 1,940 11% Data sources: Station A - San Luis & Delta-Mendota Water Authority Station B - US Geological Survey Site

91 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 89 TABLE 2b. COMPARISON OF SALINITY AND SALT LOADS, WATER YEARS FLOW-WEIGHTED ELECTRICAL CONDUCTIVITY STATION A ΜS/CM STATION B ΜS/CM SALT LOADS STATION A TONS STATION B TONS DIFFERENCE DIFFERENCE AS PERCENT OF STATION B WY ,477 4, , ,830-8,870-5% WY ,625 4, , ,110-6,220-3% WY ,821 4, , ,140 5,260 4% WY ,478 4, , , % WY ,634 4, , ,030-5,070-4% WY ,427 4, , ,190 4,990 4% WY ,552 4, , ,760 5,130 4% WY ,446 4, , ,350 5,720 5% WY ,583 4, , ,560 5,530 4% WY ,782 4, , ,020 9,950 8% WY ,660 4,235 77,140 79,700 2,560 3% WY ,151 4,120 55,350 65,930 10,580 16% WY ,827 4,254 47,840 55,590 7,750 14% WY ,266 4,617 58,460 67,670 9,210 14% WY ,211 4,498 86,450 87,520 1,070 1% WY ,006 3,847 43,240 38,430-4,810-13% WY ,386 5,524 43,420 53,920 10,500 19% WY ,230 7,449 34,430 45,070 10,640 24% TABLE 2c. COMPARISON OF SALINITY AND SALT LOADS, CALENDAR YEARS FLOW-WEIGHTED ELECTRICAL CONDUCTIVITY STATION A ΜS/CM STATION B ΜS/CM SALT LOADS STATION A TONS STATION B TONS DIFFERENCE DIFFERENCE AS PERCENT OF STATION B ,627 4, , ,330-4,920-3% ,699 4, , ,860-5,870-3% ,767 4, , ,580 7,960 5% ,379 4, , ,600-4,760-4% ,661 4, , ,210-2,250-2% ,469 4, , ,760 2,730 2% ,559 4, , ,330 5,090 4% ,404 4, , ,000 6,140 5% ,581 4, , ,060 8,390 6% ,923 4, , ,500 7,240 6% ,460 4,096 71,600 75,550 3,950 5% ,975 4,096 56,480 66,200 9,720 15% ,843 4,367 48,020 56,280 8,260 15% ,556 4,583 62,840 68,150 5,310 8% ,407 4,205 83,600 81,640-1,960-2% ,760 4,045 37,800 39,260 1,460 4% ,248 6,028 45,830 57,230 11,400 20% ,495 8,569 45,720 55,860 10,140 18% Data source: Calculated from data published by the San Francisco Estuary Institute

92 90 GRASSLAND BYPASS PROJECT TABLE 3a. COMPARISON OF SELENIUM MEASUREMENTS IN THE SAN LUIS DRAIN FLOW-WEIGHTED SELENIUM CONCENTRATION (1) STATION A ΜG/L STATION B ΜG/L TOTAL SELENIUM LOADS STATION A (2) POUNDS STATION B (3) POUNDS DIFFERENCE DIFFERENCE AS PERCENT OF STATION B January % February % March % April % May % June % July % August % September % October % November % December % January % February % March % April % May % June % July % August % September % October % November % December % January % February % March % April % May % June % July % August % September % October % November % December % Data Sources: Station A - Calculated from Regional Board weekly composite samples at Site MER562s Station B - Published by San Francisco Estuary Institute (1) Flow-weighted concentrations and loads calculated by USBR SCC-107 (2) Selenium load calculated by USBR SCC-107 (3) Selenium load published by San Francisco Estuary Institute

93 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 91 TABLE 3b. COMPARISON OF SELENIUM MEASUREMENTS WATER YEARS AVERAGE FLOW- WEIGHTED CONCENTRATION STATION A ΜG/L STATION B ΜG/L TOTAL SELENIUM LOADS STATION A POUNDS STATION B POUNDS DIFFERENCE DIFFERENCE AS PERCENT OF STATION B WY ,418 6, % WY ,436 8, % WY ,178 5, % WY ,685 4, % WY ,509 4, % WY ,815 3, % WY ,865 4, % WY ,813 3, % WY ,701 4, % WY ,612 3, % WY ,581 2, % WY ,743 1, % WY ,350 1, % WY ,686 1, % WY ,140 2, % WY % WY % WY % TABLE 3c. COMPARISON OF SELENIUM MEASUREMENTS CALENDAR YEARS AVERAGE FLOW- WEIGHTED CONCENTRATION STATION A ΜG/L STATION B ΜG/L TOTAL SELENIUM LOADS STATION A POUNDS STATION B POUNDS DIFFERENCE DIFFERENCE AS PERCENT OF STATION B ,173 6, % ,567 8, % ,018 4, % ,646 4, % ,360 4, % ,089 4, % ,868 4, % ,621 3, % ,686 4, % ,795 3, % ,267 2, % ,707 1, % ,359 1, % ,744 1, % ,969 1, % % % % Data source: Flow-weighted concentrations and loads calculated by USBR SCC-107

94 92 GRASSLAND BYPASS PROJECT TABLE 4a. GAIN OR LOSS DUE TO PRECIPITATION AND EVAPOTRANSPIRATION PRECIPITATION EVAPOTRANSPIRATION THREE SITE AVERAGE PRECIP INCHES (1) THREE SITE AVERAGE PRECIP FEET CALCULATED WATER GAIN FROM PRECIP ON SAN LUIS DRAIN ACRE FEET (2) THREE SITE AVERAGE ETO INCHES (3) THREE SITE AVERAGE ETO FEET CALCULATED WATER LOST TO EVAP. FROM SAN LUIS DRAIN ACRE FEET (4) GAIN OR LOSS FROM WATER SURFACE OF SAN LUIS DRAIN ACRE FEET (5) FLOW PASSING STATION A ACRE FEET (6) FLOW PASSING STATION B ACRE FEET (7) DIFFERENCE IN FLOW PASSING STATIONS A AND B ACRE FEET (8) NET WATER GAIN/ LOSS NOT DUE TO PRECIP OR ETO ACRE FEET (9) EQUIVALENT FLOW RATE CFS (10) NET WATER GAIN/LOSS AS PERCENT OF SITE B FLOW PERCENT (11) JAN % FEB , % MAR ,240 1, % APR % MAY % JUN % JUL % AUG % SEP % OCT % NOV % DEC , % JAN , % FEB , % MAR % APR % MAY % JUN % JUL % AUG % SEP % OCT % NOV % DEC % JAN % FEB ,040 1, %

95 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 93 TABLE 4a. GAIN OR LOSS DUE TO PRECIPITATION AND EVAPOTRANSPIRATION (CONTIN.) PRECIPITATION EVAPOTRANSPIRATION THREE SITE AVERAGE PRECIP INCHES (1) THREE SITE AVERAGE PRECIP FEET CALCULATED WATER GAIN FROM PRECIP ON SAN LUIS DRAIN ACRE FEET (2) THREE SITE AVERAGE ETO INCHES (3) THREE SITE AVERAGE ETO FEET CALCULATED WATER LOST TO EVAP. FROM SAN LUIS DRAIN ACRE FEET (4) GAIN OR LOSS FROM WATER SURFACE OF SAN LUIS DRAIN ACRE FEET (5) FLOW PASSING STATION A ACRE FEET (6) FLOW PASSING STATION B ACRE FEET (7) DIFFERENCE IN FLOW PASSING STATIONS A AND B ACRE FEET (8) NET WATER GAIN/ LOSS NOT DUE TO PRECIP OR ETO ACRE FEET (9) EQUIVALENT FLOW RATE CFS (10) NET WATER GAIN/LOSS AS PERCENT OF SITE B FLOW PERCENT (11) MAR % APR % MAY % JUN % JUL % AUG % SEP % OCT % NOV % DEC ,446 2, % Notes: (1) California Irrigation Management Information System - Average preciptiation for Stations 007, 056, and 124 (7) Flow passing Station B (from Table 1) (2) Total rainfall x SLD surface area. SLD surface area = 28 mi x 30' top width = ac (8) Flow at Station B - Flow at Station A (3) California Irrigation Management Information System - Average Eto for Stations 007, 056, and 124 (9) Column (8) - (5) = Net water volume gained from or lost (4) Total evapotranspiration from the SLD surface area (101.8 acres) (10) Average daily flow (cfs) of the Net Water Gain/Loss (5) Sum of rainfall and evapotransipration from the SLD (11) Difference in flow (6)/ Station B flow x 100%

96 94 GRASSLAND BYPASS PROJECT TABLE 4b. GAIN OR LOSS DUE TO PRECIPITATION AND EVAPOTRANSPIRATION, WATER YEAR TOTALS THREE SITE AVERAGE PRECIP INCHES THREE SITE AVERAGE PRECIP FEET WATER GAIN FROM PRECIP ON SAN LUIS DRAIN ACRE FEET THREE SITE AVERAGE ETO INCHES THREE SITE AVERAGE ETO FEET WATER LOST TO EVAP. FROM SAN LUIS DRAIN ACRE FEET GAIN OR LOSS FROM WATER SURFACE ACRE FEET FLOW PASSING STATION A ACRE FEET FLOW PASSING STATION B ACRE FEET DIFFERENCES IN FLOWS PASSING STATIONS A AND B ACRE FEET NET WATER GAIN/LOSS NOT DUE TO PRECIP OR ETO ACRE FEET EQUIVALENT FLOW RATE CFS NET WATER GAIN/LOSS AS PERCENT OF SITE B FLOW PERCENT WY ,800 37, % WY ,570 45,950 2,380 2, % WY ,510 32,310 1,800 1, % WY ,330 31,260 1,930 1, % WY ,050 28,250 1, % WY ,820 28,400 2,580 2, % WY ,250 27,270 2,020 1, % WY ,370 27,700 2,330 1, % WY ,940 28,370 2,430 2, % WY ,080 25,970 2,890 2, % WY ,480 18,540 2,060 1, % WY ,230 15,670 2,440 1, % WY ,340 13, % WY ,610 14, % WY ,540 18,510 1,970 1, % WY ,620 10,490 1,870 1, % WY ,010 10,040 2,030 1, % WY ,754 7,133 2,379 2, %

97 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 95 TABLE 4c. GAIN OR LOSS DUE TO PRECIPITATION AND EVAPOTRANSPIRATION, CALENDAR YEAR TOTALS THREE SITE AVERAGE PRECIP INCHES CIMIS PRECIPITATION CIMIS EVAPOTRANSPIRATION THREE SITE AVERAGE PRECIP FEET WATER GAIN FROM PRECIP ON SAN LUIS DRAIN ACRE FEET THREE SITE AVERAGE ETO INCHES THREE SITE AVERAGE ETO FEET WATER LOST TO EVAP. FROM SAN LUIS DRAIN ACRE FEET GAIN OR LOSS FROM WATER SURFACE ACRE FEET FLOW PASSING STATION A ACRE FEET FLOW PASSING STATION B ACRE FEET DIFFERENCES IN FLOWS PASSING STATIONS A AND B ACRE FEET NET WATER GAIN/ LOSS NOT DUE TO PRECIP OR ETO ACRE FEET EQUIVALENT FLOW RATE CFS NET WATER GAIN/ LOSS AS PERCENT OF SITE B FLOW PERCENT ,590 37, % ,220 46,240 2,020 1, % ,910 32,250 2,340 1, % ,920 30,210 1, % ,190 28,010 1,820 1, % ,520 28,460 1,940 1, % ,360 27,550 2,190 1, % ,730 28,290 2,560 2, % ,870 29,610 2,740 2, % ,180 25,890 2,710 2, % ,760 17,990 2,230 1, % ,880 15,860 1,980 1, % ,340 13, % ,610 14, % ,650 18,020 2,370 1, % ,910 10,020 2,110 1, % ,750 9,710 1,960 1, % ,573 8,350 1,777 1, %

98 96 GRASSLAND BYPASS PROJECT TABLE 5a. SUMMARY MASS BALANCE IN THE SAN LUIS DRAIN DIFFERENCE IN FLOW BETWEEN SITES A AND B DIFFERENCE IN SALT LOAD BETWEEN SITES A AND B DIFFERENCE IN SELENIUM LOAD BETWEEN SITES A AND B DIFFERENCE IN FLOW NOT DUE TO RAIN OR EVAPOTRANSPIRATION Table 1a Table 2a Table 3a Table 4a January % -15% 24% 38% February % 12% -8% 27% March % -14% -4% 14% April % -36% -38% -9% May % -5% -33% -20% June % 5% -9% -19% July % -16% -21% -18% August % 0% -14% -14% September % 43% 23% 32% October % 49% 12% 59% November % 42% 6% 55% December % 12% -2% 32% January % 22% -1% 33% February % 20% 20% 21% March % 12% -5% 7% April % 11% -25% -11% May % 21% -30% -12% June % 16% -4% -21% July % 0% -50% -13% August % 14% -23% -3% September % 37% 7% 18% October % 31% 5% 43% November % 30% -5% 52% December % 28% -49% 53% January % 13% -15% 32% February % 11% 1% 17% March % 26% 25% 31% April % 13% -105% 19% May % 40% -53% 18% June % 10% -32% -14% July % 38% -91% 5% August % 74% 33% -37% September % 80% 63% -38% October % 86% 88% 33% November % 14% 27% 24% December % 11% -4% 14% TABLE 5b. SAN LUIS DRAIN MASS BALANCE - SUMMARY STATISTICS DIFFERENCE IN FLOW BETWEEN SITES A AND B DIFFERENCE IN SALT LOAD BETWEEN SITES A AND B DIFFERENCE IN SELENIUM LOAD BETWEEN SITES A AND B DIFFERENCE IN FLOW NOT DUE TO RAIN OR EVAPOTRANSPIRATION Maximum 80% 86% 88% 59% Month Oct-14 Oct-14 Dec-14 Oct-12 Minimum -23% -56% -172% -38% Month Jul-10 Dec-11 Nov-12 Sep-14 Median 8% 6% -0.8% 5% Average 12% 7% -3.9% 9% Count

99 FIGURE 1. MAP OF THE GRASSLAND BYPASS PROJECT CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 97

100 98 GRASSLAND BYPASS PROJECT FIGURE 2. GRASSLAND BYPASS PROJECT - SCHEMATIC DIAGRAM SHOWING LOCATIONS OF GBP MONITORING SITES RELATIVE TO MAJOR HYDROLOGIC FEATURES OF THE STUDY AREA N Merced River H (Seasonal) Mud Slough (north) E I D C B G San Luis Drain San Joaquin River F Salt Slough Fremont Canal San Luis Canal Santa Fe Canal San Luis Canal North Grassland Water District L2 M2 Santa Fe Canal San Luis Drain Blake-Porter Bypass Wetland water supply Camp 13 Canal South Grassland Water District J K Agatha Canal A Grassland Bypass Main Canal (via DMC and Mendota Pool) Agricultural Water Districts

101 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 99 FIGURE 3a. COMPARISON OF FLOWS IN THE SAN LUIS DRAIN Flow (acre-feet / month) Jan-12 Feb-12 Mar-12 Apr-12 May-12 Jun-12 Jul-12 Aug-12 Sep-12 Oct-12 Nov-12 Dec FIGURE 3b. COMPARISON OF FLOWS IN THE SAN LUIS DRAIN Flow (acre-feet / month) Jan-13 Feb-13 Mar-13 Apr-13 May-13 Jun-13 Jul-13 Aug-13 Sep-13 Oct-13 Nov-13 Dec-13

102 100 GRASSLAND BYPASS PROJECT FIGURE 3c. COMPARISON OF FLOWS IN THE SAN LUIS DRAIN Flow (acre-feet / month) Jan-14 Feb-14 Mar-14 Apr-14 May-14 Jun-14 Jul-14 Aug-14 Sep-14 Oct-14 Nov-14 Dec-14 FIGURE 4a. COMPARISON OF SALT LOADS IN THE SAN LUIS DRAIN ,500 1,310 Gain or Loss between Sites A and B 1,120 1, ,000-1,030-1,500 Jan-12 Feb-12 Mar-12 Apr-12 May-12 Jun-12 Jul-12 Aug-12 Sep-12 Oct-12 Nov-12 Dec-12 Salt Load (tons/month)

103 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 101 FIGURE 4b. COMPARISON OF SALT LOADS IN THE SAN LUIS DRAIN ,000 1,890 Gain or Loss between Sites A and B 1,500 1,540 1,170 1,130 1,180 1,000 1, Salt Load (tons/month) Jan-13 Feb-13 Mar-13 Apr-13 May-13 Jun-13 Jul-13 Aug-13 Sep-13 Oct-13 Nov-13 Dec-13 FIGURE 4c. COMPARISON OF SALT LOADS IN THE SAN LUIS DRAIN ,000 1,890 Gain or Loss between Sites A and B 1,500 1,540 1,170 1,130 1,180 1,000 1, Jan-13 Feb-13 Mar-13 Apr-13 May-13 Jun-13 Jul-13 Aug-13 Sep-13 Oct-13 Nov-13 Dec-13 Salt Load (tons/month)

104 102 GRASSLAND BYPASS PROJECT FIGURE 5a. COMPARISON OF SELENIUM LOADS IN THE SAN LUIS DRAIN Selenium Load (pounds/month) Gain or Loss between Sites A and B Jan-12 Feb-12 Mar-12 Apr-12 May-12 Jun-12 Jul-12 Aug-12 Sep-12 Oct-12 Nov-12 Dec-12 FIGURE 5b. COMPARISON OF SELENIUM LOADS IN THE SAN LUIS DRAIN Selenium Load (pounds/month) Jan-13 Feb-13 Mar-13 Apr-13 May-13 Jun-13 Jul-13 Aug-13 Sep-13 Oct-13 Nov-13 Dec-13 Gain or Loss between Sites A and B

105 CHAPTER 5: FLOW, SALT AND SELENIUM MASS BALANCES IN THE SAN LUIS DRAIN 103 FIGURE 5c. COMPARISON OF SELENIUM LOADS IN THE SAN LUIS DRAIN Selenium Load (pounds/month) Jan-14 Feb-14 Mar-14 Apr-14 May-14 Jun-14 Jul-14 Aug-14 Sep-14 Oct-14 Nov-14 Dec-14 Gain or Loss between Sites A and B

106 104 GRASSLAND BYPASS PROJECT

107 06 PROJECT CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER IMPACTS ON THE SAN JOAQUIN RIVER 105 Michael C. S. Eacock1 Jeffrey E. Papendick 2 Nigel W.T. Quinn3 1 Natural Resource Specialist, US Bureau of Reclamation, South-Central California Area Office, 1243 N Street, Fresno, California meacock@usbr.gov 2 Natural Resources Technician, South-Central California Area Office, 1243 N Street, Fresno, California jpapendick@usbr.gov 3 Staff Geological Scientist/Water Resources Engineer, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Building 70A-3317H, Berkeley, California nquinn@lbl.gov INTRODUCTION The purpose of this chapter is to compare the loads of salt discharged by the Grassland Bypass Project (GBP) with loads that might exist in the absence of the project. This comparison uses flow and salinity data for stations in the San Luis Drain, Mud Slough, Salt Slough, and the San Joaquin River from October 1985 to December Two methods are used: simple comparison of flow and salt loads as percentages, and theoretical dilution analysis. The theoretical dilution analysis was agreed upon in meetings involving the US Bureau of Reclamation (Reclamation), the South Delta Water Agency and its legal counsel, and the California Regional Water Quality Control Board, as a means of demonstrating that the Project was not causing adverse downstream impacts. Section D of the 2009 Use Agreement includes the following statement: It is the intention and objective of RECLAMATION and the AUTHORITY, among other things, to ensure that continued use of the Drain as provided in this Agreement results in improvement in water quality and environmental conditions in the San Joaquin River, delta, and estuary relative to the quality that existed prior to the term of this Agreement, insofar as such quality or conditions may be affected by drainage discharges from the Drainage Area (as hereinafter defined), and to ensure that such continued use of the Drain does not reduce the ability to meet the salinity standard at Vernalis compared to the ability to meet the salinity standard that existed prior to the term of this Agreement. COMPARISON OF FLOW AND SALT LOADS AS PERCENTAGES Table 1a compares the monthly flows and loads of salt discharged by the Project (measured at station B) with those in the San Joaquin River at Crows Landing (station N) during During Water Year (WY) 2012, the Project contributed two percent of the flow passing Crows Landing, and eight percent of the monthly salt load in the river (Table 1b). During WY 2013, the Project contributed three percent of the flow and fourteen percent of the salts in the river. During WY 2014, the Project contributed three percent of the flow and seventeen percent of the salts in the river. During the entire eighteen years of the Project, the Project has contributed between one and five percent of the annual flow and up to 22 percent of the salt load in the river as measured at Crows Landing (Table 1b). Table 2 compares the volumes of water discharged from the 97,000 acre Grassland Drainage Area (GDA) with flows in the Grasslands watershed, as measured in Mud and Salt Sloughs. Prior to WY 1997, the uncontrolled volume of water discharged from the GDA was 20 to 32 percent of the regional flow. Under the Grassland Bypass Project, flow from the GDA was reduced to nine percent of the annual regional flow during WY 2013.

108 106 GRASSLAND BYPASS PROJECT Table 3 compares the loads of salts discharged from the GDA with the salts in water in Mud and Salt Sloughs. Prior to WY 1997, the uncontrolled flow from the GDA contributed forty-one to fifty-nine percent of the regional salt load. The Grassland Bypass Project has reduced the salt load to an average of thirty percent, ranging from 38 percent during WY 1997 (wet) and 16 percent during WY 2012 (dry). 1 is a map that shows the location of the monitoring stations along the San Luis Drain and tributaries of the San Joaquin River. Figure 2 is a schematic diagram of the Project with the location of monitoring stations discussed in this report. THEORETICAL DILUTION OF GBP DISCHARGES TO MEET VERNALIS STANDARDS In order to assess the effect of GBP on salinity in the San Joaquin River, a model was developed to theoretically isolate the effects of GBP from other activities potentially affecting salinity concentrations in the river. Drainage from GBP was assumed as the only drainage relevant to project related changes in salt load on the San Joaquin River. The model was cast in terms of theoretical dilution water needed to bring the GBP discharges to the Vernalis seasonal salinity objectives. The salinity objectives for Vernalis are 1,000 μs/cm (640 mg/l Total Dissolved Solids) in the winter months (September March) and 700 μs/cm (448 mg/l TDS) in the summer months (April August). Table 4 lists the theoretical volume of water that would be needed each year to dilute the combined salt loads from the GDA, measured at station A, and the Grasslands Watershed, drained by Mud Slough and Salt Slough (stations D & F), to meet the Vernalis standards. This analysis does not take into account any of the other operational criteria, nor does it consider salinity contributions to the River other than those derived from the GDA. The value of the analysis is that it permits a "with" and "without" project comparison with prior year hydrology, in terms (water quality releases from a reservoir) meaningful to water users and managers. The assimilative capacity analysis considers the total volume of dilution water (assumed to have a salinity of 100 mg/l) that would be needed to reduce the drainage water alone to the salinity objective. Note that the monthly volume of dilution water is highly dependent on the 100 mg/l assumption. Note also that the relation between dilution water quality and required volume is non linear. Figure 3 shows the monthly theoretical dilution requirements for October 1985 through December Figure 4 shows the total theoretical dilution requirement for Water Years The red areas in Figures 1 and 2 represent the theoretical dilution requirements for salt loads generated by the Grasslands Watershed which includes the GDA and other agricultural areas, wetlands, and uncontrolled runoff from the Coast Range watersheds. The blue areas in both figures shows the theoretical dilution requirements for salt loads discharged from only the GDA. The data for Figure 3 are summarized in Table 4. Prior to WY 1997, an annual average of 273,440 acre-feet of water from New Melones would have been needed to dilute the uncontrolled annual volume of drainage water discharged from the GDA to meet the Vernalis standard. During the eighteen years of the Project, this theoretical dilution annual volume of water was been steadily reduced; the 2014 theroretical dilution volume would have been only 47,000 acre-feet. These values should be put into context of the drought and the initiation of CVPIA water deliveries to wetlands (private, State and Federal) in the Grasslands Basin that preceded the authorization of the Grassland Bypass Project. The latter has affected the hydrology of the Grasslands Basin and has affected the timing of salt loading to the San Joaquin River. WY 2012 was classified as a dry year and WY 2013 and WY 2014 were classified as a critical year. The theoretical volumes of water needed to dilute the water from the GDA are less than the theoretical volumes needed during the dry and critical drought years of (Table 4 and Figure 2). We will continue the compile these data to assess the impact of the GBP on the San Joaquin River, as measured by dilution requirements for GDA discharges (station A) and for the regional watershed.

109 CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER 107 CALCULATIONS The formula for theoretical dilution is: Q2 = Q1 * (C3-C1)/(C2-C3) Q1 =Drainwater discharge in acre-feet per month Q2 = Volume of water needed to dilute Q1 to meet Vernalis standards in acre-feet per month C1 =Measured concentration of GBP drainage water in parts per million (mg/l) C2 =Assumed concentration of dilution water = 100 mg/l C3 =Vernalis standard concentration = 448 mg/l April - August = 640 mg/l September March TABLES Tables 1a,b,c. Comparison of Flows and Salt Loads Discharged to the San Joaquin River Table 2. Annual Volume of Water Discharged from the Grassland Drainage Area and Mud/Salt Slough Table 3. Annual Loads of Salt Discharged from the Grassland Drainage Area and Mud/Salt Slough Table 4. Theoretical Annual Volumes of Dilution Water Needed to Meet Vernalis Standards FIGURES Figure 1. Map of the Grassland Bypass Project Figure 2. Grassland Bypass Project - Schematic Diagram Showing Locations of GBP Monitoring Stations Relative to Major Hydrologic Features of the Study Area Figure 3. Theoretical Monthly Volumes of Water Needed to Dilute Drainage Water from the Grasslands Drainage Area and the Regional Watershed to Meet Vernalis Figure 4. Theoretical Annual Volumes of Water Needed to Dilute Drainage from the Grassland Drainage Area and the Regional Watershed to Meet Vernalis

110 108 GRASSLAND BYPASS PROJECT TABLE 1a. COMPARISON OF FLOWS AND SALT LOADS DISCHARGED TO THE SAN JOAQUIN RIVER MONTHLY FLOW MONTHLY SALT LOAD GRASSLAND BYPASS PROJECT STATION B ACRE-FEET SAN JOAQUIN RIVER AT CROWS LANDING STATION N ACRE-FEET B AS % OF N GRASSLAND BYPASS PROJECT STATION B TONS SAN JOAQUIN RIVER AT CROWS LANDING STATION N TONS B AS % OF N January ,280 3% 2,560 44,840 6% February ,160 36,700 3% 3,310 48,730 7% March ,460 49,010 3% 5,380 67,610 8% April ,360 2% 2,900 49,780 6% May ,260 1% 3,170 31,830 10% June ,460 3% 3,800 28,690 13% July ,640 3% 3,920 23,610 17% August ,470 3% 2,700 19,500 14% September ,690 2% 1,920 16,810 11% October ,700 2% 2,270 21,990 10% November ,330 3% 3,100 26,950 12% December ,050 61,100 2% 5,240 44,620 12% January ,150 54,290 2% 5,300 51,740 10% February ,060 34,080 3% 5,030 42,830 12% March ,820 2% 4,730 56,220 8% April ,020 2% 4,880 38,250 13% May ,370 3% 4,260 27,490 15% June ,690 3% 3,630 24,010 15% July ,380 5% 5,260 19,550 27% August ,100 5% 6,110 18,160 34% September ,570 2% 5,120 18,200 28% October ,670 3% 4,970 23,950 21% November ,800 2% 3,780 27,920 14% December ,630 3% 4,150 30,437 14% January ,200 4% 5,320 30,160 18% February ,270 22,450 6% ,330 23% March ,480 4% 5,410 39,870 14% April ,730 2% 3,270 29,930 11% May ,060 4% 2,790 17,580 16% June ,040 7% 3,300 9,480 35% July ,200 8% 3,420 6,060 56% August ,080 1% 430 5,110 8% September ,560 1% 410 6,200 7% October ,580 0% ,510 7% November ,500 3% 5,430 13,540 40% December ,840 36,470 8% 17,500 40,580 43% Data Sources: Station B - SLDMWA data, formerly US Geological Survey Site Station N - US Geological Survey Site

111 CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER 109 TABLE 1b. COMPARISON OF FLOWS AND SALT LOADS DISCHARGED TO THE SAN JOAQUIN RIVER, WATER YEARS TOTAL FLOW TOTAL SALT LOAD TOTAL FLOW GRASSLAND BYPASS PROJECT STATION B ACRE-FEET SAN JOAQUIN RIVER AT CROWS LANDING STATION N ACRE-FEET B AS % OF N TOTAL SALT LOAD GRASSLAND BYPASS PROJECT STATION B TONS SAN JOAQUIN RIVER AT CROWS LANDING STATION N TONS B AS % OF N WY ,560 3,844,610 1% 167,830 1,067,030 16% WY ,950 4,904,910 1% 205,110 1,493,450 14% WY ,310 1,015,480 3% 149, ,840 22% WY ,260 1,027,440 3% 135, ,370 19% WY , ,430 4% 120, ,060 19% WY , ,960 5% 116, ,580 22% WY , ,130 5% 118, ,350 21% WY , ,550 5% 116, ,890 21% WY ,160 1,721,000 2% 132, ,230 15% WY ,970 3,437,650 1% 119, ,840 13% WY , ,360 3% 77, ,580 15% WY , ,030 3% 65, ,050 13% WY , ,670 4% 55, ,510 15% WY , ,070 2% 67, ,320 13% WY ,510 3,192,490 1% 87, ,640 10% WY , ,230 2% 38, ,370 8% WY , ,450 3% 54, ,010 14% WY , ,900 3% 45, ,027 17% TABLE 1b. COMPARISON OF FLOWS AND SALT LOADS DISCHARGED TO THE SAN JOAQUIN RIVER, WATER YEARS TOTAL FLOW TOTAL SALT LOAD GRASSLAND BYPASS PROJECT STATION B ACRE-FEET SAN JOAQUIN RIVER AT CROWS LANDING STATION N ACRE-FEET B AS % OF N GRASSLAND BYPASS PROJECT STATION B TONS SAN JOAQUIN RIVER AT CROWS LANDING STATION N TONS B AS % OF N ,490 3,590,680 1% 169,330 1,060,870 16% ,240 5,064,330 1% 208,860 1,497,060 14% , ,600 4% 146, ,970 22% ,210 1,059,180 3% 128, ,060 19% , ,210 4% 119, ,700 19% , ,240 5% 117, ,650 22% , ,480 5% 119, ,560 21% , ,270 5% 118, ,090 21% ,610 1,755,440 2% 132, ,950 15% ,890 3,463,050 1% 116, ,470 12% , ,850 3% 75, ,770 15% , ,470 3% 66, ,340 14% , ,380 4% 56, ,910 15% , ,230 2% 68, ,840 12% ,020 3,177,990 1% 81, ,550 10% , ,000 2% 40, ,960 9% , ,420 3% 57, ,757 15% , ,350 4% 55, ,350 23%

112 110 GRASSLAND BYPASS PROJECT TABLE 2. ANNUAL VOLUME OF WATER DISCHARGED FROM THE GRASSLAND DRAINAGE AREA AND MUD/SALT SLOUGH WATERSHED WATER YEAR (1) WATER YEAR TYPE WATER DISCHARGED FROM GRASSLAND DRAINAGE AREA (2) ACRE-FEET WATER DISCHARGED FROM MUD AND SALT SLOUGHS (3) ACRE-FEET GDA DISCHARGE AS PERCENT OF DISCHARGE FROM THE SLOUGHS WY 1986 Wet 67, ,320 24% WY 1987 Critical 74, ,840 32% WY 1988 Critical 65, ,450 28% WY 1989 Critical 54, ,390 26% WY 1990 Critical 41, ,660 21% WY 1991 Critical 29, ,160 29% WY 1992 Critical 24,530 85,430 29% WY 1993 Wet 41, ,960 25% WY 1994 Critical 38, ,550 21% WY 1995 Wet 57, ,770 22% WY 1996 Wet 52, ,950 20% WY 1997 Wet 37, ,010 13% WY 1998 Wet 45, ,670 12% WY 1999 Above Normal 32, ,130 13% WY 2000 Above Normal 31, ,490 13% WY 2001 Dry 28, ,750 12% WY 2002 Dry 28, ,160 16% WY 2003 Below Normal 27, ,140 13% WY 2004 Dry 27, ,520 13% WY 2005 Wet 30, ,880 11% WY 2006 Wet 25, ,000 9% WY 2007 Critical 18, ,330 10% WY 2008 Critical 15, ,670 10% WY 2009 Below Normal 13, ,510 12% WY 2010 Above Normal 14, ,580 9% WY 2011 Wet 18, ,270 8% WY 2012 Dry 10, ,200 7% WY 2013 Critical 10, ,350 6% WY 2014 Critical 7,130 76,750 9% Before GBP average (WY ) 49, ,320 25% GBP average (WY ) 23, ,250 11% Average, Dry Water Years (4) 36, ,190 21% Average, Wet Water Years (5) 37, ,170 15% Notes: Pre-project data compiled by Nigel Quinn (LBNL) from CVRWQCB and USGS reports. (1) Water Year - October 1 - September 30 (2) Grassland Drainage Area GDA WY : CVRWQCB data GDA WY : Station B - San Luis Drain, LBL, USGS, and SLDMWA data (3) Mud and Salt Sloughs Station D - Mud Slough near Gustine, US Geological Survey Site Station F - Salt Slough at Hwy 165, US Geological Survey Site (4) Below Normal, Critical, and Dry Water Years: , 1994, 2001, 2002, 2004, 2007, 2008, 2009,2012, 2013,2014 (5) Above Normal and Wet Water Years: WY 1986, 1993, , 2003, 2005, 2006, 2010, 2011

113 CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER 111 TABLE 3. ANNUAL LOADS OF SALT DISCHARGED FROM THE GRASSLAND DRAINAGE AREA AND MUD/SALT SLOUGH WATERSHED WATER YEAR (1) WATER YEAR TYPE SALT DISCHARGED FROM GRASSLAND DRAINAGE AREA (2) TONS SALT DISCHARGED FROM MUD AND SALT SLOUGHS (3) TONS GDA SALT DISCHARGE AS PERCENT OF DISCHARGE FROM THE SLOUGHS WY 1986 Wet 214, ,540 43% WY 1987 Critical 241, ,900 55% WY 1988 Critical 236, ,960 52% WY 1989 Critical 202, ,330 52% WY 1990 Critical 171, ,560 45% WY 1991 Critical 129, ,540 59% WY 1992 Critical 110, ,350 56% WY 1993 Wet 183, ,520 54% WY 1994 Critical 171, ,410 45% WY 1995 Wet 237, ,340 48% WY 1996 Wet 197, ,730 41% WY 1997 Wet 167, ,700 38% WY 1998 Wet 205, ,660 33% WY 1999 Above Normal 149, ,620 37% WY 2000 Above Normal 135, ,430 36% WY 2001 Dry 120, ,150 31% WY 2002 Dry 116, ,350 35% WY 2003 Below Normal 118, ,930 32% WY 2004 Dry 116, ,500 33% WY 2005 Wet 132, ,440 30% WY 2006 Wet 121, ,860 28% WY 2007 Critical 79, ,590 30% WY 2008 Critical 65, ,040 25% WY 2009 Below Normal 55, ,420 29% WY 2010 Above Normal 67, ,360 24% WY 2011 Wet 87, ,310 24% WY 2012 Dry 38, ,050 16% WY 2013 Critical 53, ,860 21% WY 2014 Critical 44, ,600 29% Before GBP average (WY ) 190, ,290 49% GBP average (WY ) 104, ,940 30% Average, Dry Water Years (4) 126, ,030 40% Average, Wet Water Years (5) 158, ,980 35% Notes: Pre-project data compiled by Nigel Quinn (LBNL) from CVRWQCB and USGS reports. (1) Water Year - October 1 - September 30 (2) Grassland Drainage Area GDA WY : CVRWQCB data GDA WY : Station B - San Luis Drain, LBL, USGS, and SLDMWA data (3) Mud and Salt Sloughs Station D - Mud Slough near Gustine, US Geological Survey Site Station F - Salt Slough at Hwy 165, US Geological Survey Site (4) Below Normal, Critical, and Dry Water Years: , 1994, 2001, 2002, 2004, 2007, 2008, 2009, 2012, 2013,2014 (5) Above Normal and Wet Water Years: WY 1986, 1993, , 2003, 2005, 2006, 2010, 2011

114 112 GRASSLAND BYPASS PROJECT TABLE 4. THEORETICAL ANNUAL VOLUMES OF DILUTION WATER NEEDED TO MEET VERNALIS STANDARDS WATER YEAR (1) WATER YEAR TYPE THEORETICAL ANNUAL VOLUME OF WATER NEEDED TO DILUTE GDA DISCHARGE TO MEET VERNALIS STANDARD (2) ACRE-FEET THEORETICAL ANNUAL VOLUME WATER NEEDED TO DILUTE REGIONAL DISCHARGE TO MEET VERNALIS STANDARD (3) ACRE-FEET WY 1986 Wet 303, ,150 WY 1987 Critical 332, ,130 WY 1988 Critical 335, ,450 WY 1989 Critical 294, ,410 WY 1990 Critical 245, ,300 WY 1991 Critical 186, ,850 WY 1992 Critical 160, ,070 WY 1993 Wet 272, ,960 WY 1994 Critical 249, ,090 WY 1995 Wet 344, ,510 WY 1996 Wet 283, ,390 WY 1997 Wet 243, ,720 WY 1998 Wet 294, ,350 WY 1999 Above Normal 201, ,520 WY 2000 Above Normal 190, ,220 WY 2001 Dry 174, ,700 WY 2002 Dry 154, ,060 WY 2003 Below Normal 158, ,370 WY 2004 Dry 151, ,940 WY 2005 Wet 172, ,960 WY 2006 Wet 153, ,330 WY 2007 Critical 104, ,730 WY 2008 Critical 73, ,920 WY 2009 Below Normal 60, ,150 WY 2010 Above Normal 80, ,830 WY 2011 Wet 118, ,310 WY 2012 Dry 58, ,190 WY 2013 Critical 61, ,400 WY 2014 Critical 47, ,390 Before GBP average (WY ) 273, ,660 GBP average (WY ) 138, ,890 Average, Dry Water Years (4) 175, ,800 Average, Wet Water Years (5) 221, ,940 Notes: Pre-project data compiled by Nigel Quinn (LBNL) from CVRWQCB and USGS reports. (1) Water Year = October 1 - September 30 (2) Grassland Drainage Area GDA WY : CVRWQCB data GDA WY : Station B - San Luis Drain, LBL, USGS, and SLDMWA data (3) Mud and Salt Sloughs Station D - Mud Slough near Gustine, US Geological Survey Site Station F - Salt Slough at Hwy 165, US Geological Survey Site (4) Below Normal, Critical, and Dry Water Years: , 1994, 2001, 2002, 2004, 2007, 2008, 2009, 2012,2013, 2014 (5) Above Normal and Wet Water Years: WY 1986, 1993, , 2003, 2005, 2006, 2010, 2011

115 FIGURE 1. MAP OF THE GRASSLAND BYPASS PROJECT CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER 113

116 114 GRASSLAND BYPASS PROJECT FIGURE 2. GRASSLAND BYPASS PROJECT - SCHEMATIC DIAGRAM SHOWING LOCATIONS OF GBP MONITORING SITES RELATIVE TO MAJOR HYDROLOGIC FEATURES OF THE STUDY AREA N Merced River H (Seasonal) Mud Slough (north) E I D C B G San Luis Drain San Joaquin River F Salt Slough Fremont Canal San Luis Canal Santa Fe Canal San Luis Canal North Grassland Water District L2 M2 Santa Fe Canal San Luis Drain Blake-Porter Bypass Wetland water supply Camp 13 Canal South Grassland Water District J K Agatha Canal A Grassland Bypass Main Canal (via DMC and Mendota Pool) Agricultural Water Districts

117 CHAPTER 6: PROJECT IMPACTS ON THE SAN JOAQUIN RIVER 115 FIGURE 3. THEORETICAL MONTHLY VOLUMES OF WATER NEEDED TO DILUTE DRAINAGE WATER FROM THE GRASSLAND DRAINAGE AREA AND REGIONAL WATERSHED TO MEET VERNALIS SALINITY STANDARDS 100,000 90,000 80,000 Regional Watershed Grassland Drainage Area March ,530 acre-feet 70,000 Grassland Bypass Project 60,000 Acre-feet/month 50,000 40,000 30,000 20,000 10, FIGURE 4. THEORETICAL ANNUAL VOLUMES OF WATER NEEDED TO DILUTE DRAINAGE FROM THE GRASSLAND DRAINAGE AREA AND THE REGIONAL WATERSHED TO MEET VERNALIS SALINITY STANDARDS 600,000 Regional Watershed 500,000 Grassland Drainage Area Grassland Bypass Project 400, , , , Acre-feet

118 116 GRASSLAND BYPASS PROJECT

119 7a BIOLOGICAL CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 117 William N. Beckon, Ph.D.1 1 Fish and Wildlife Biologist, US Fish and Wildlife Service, Environmental Contaminants Division, Sacramento Fish and Wildlife Office, 2800 Cottage Way, Sacramento, California (916) william_beckon@fws.gov ABSTRACT In its sixteenth, seventeenth, and eighteenth years of operation ( ) the Grassland Bypass Project continued to reduce the risk of selenium toxicity in the ecosystem from which the Project removed agricultural subsurface drainwater. However, it also continued to cause elevated risk in the waterway (Mud Slough North) into which the drainwater has been diverted by the Project. Selenium concentrations in aquatic organisms in Mud Slough North reached some of the highest levels measured since the start of the Project. Many of these concentrations exceeded toxicity thresholds. Eighteen years after the Grassland Bypass Project removed drainwater discharges from Salt Slough, that waterway, which supplies refuge wetlands, continued to show a general trend of improvement. In 2014, selenium concentrations in fish and invertebrates as well as ambient water in Salt Slough reached historic lows. The overall selenium hazard (Lemly index) to the Salt Slough ecosystem has remained low from 2008 through In Mud Slough North below the outfall of the San Luis Drain (SLD), where the Project negatively affects the environment, loads and concentrations of selenium in water generally have been reduced, but selenium concentrations in aquatic organisms generally have not tracked that improvement in water quality. In the three years of this reporting period ( ) increasing numbers of aquatic organisms in this reach of Mud Slough reached toxic concentrations of selenium. The Lemly index of selenium hazard to the aquatic ecosystem has remained high from 1997 through INTRODUCTION Project History In 1985, the San Luis Drain (SLD) was closed due to deaths and developmental abnormalities of waterbirds at a reservoir in the Kesterson National Wildlife Refuge at the terminus of the SLD. The SLD, constructed by the U.S. Bureau of Reclamation (USBR), had been conceived as a means to dispose of agricultural drainwater generated from irrigation with water supplied by the federal Central Valley Water Project. However, due to environmental concerns and budget constraints, the SLD had never been completed as originally planned. The constructed portion of the SLD had been used only to convey agricultural drainwater from Westlands Water District in the western San Joaquin Valley. Farms in the adjacent Grassland Drainage Area (GDA) never used the SLD, but discharged agricultural drainwater through wetland channels in the Grassland Water District, San Luis National Wildlife Refuge Complex, and the China Island Unit of the North Grasslands Wildlife Area (Refuges) to the San Joaquin River. This drainwater contains elevated concentrations of selenium, boron, chromium, and molybdenum, and high concentrations of various salts (CEPA, 2000) that disrupt the normal ionic balance of affected aquatic ecosystems (SJVDP, 1990b). Discharge of agricultural drainwater from GDA farms was unaffected by the closure of the SLD, and drainage continued to contaminate Refuge water delivery channels after the closure of the SLD and Kesterson Reservoir in To address this problem, a proposal to use a portion of the SLD and extend it to Mud Slough, a natural waterway in the Refuges, was implemented by the USBR in September 1996 with support from other federal and state agencies (USBR, 1995; USBR and SLDMWA 1995; USBR et al., 1995). This project, known as the Grassland Bypass Project (GBP), diverts agricultural drainwater from GDA farms into the lower 28 miles of the SLD and thence into the lower portion of Mud Slough (about six miles). The GBP has removed drainwater from more than 90 miles of wetland

120 118 GRASSLAND BYPASS PROJECT water supply channels, including Salt Slough, and allows the Refuges full use of water rights to create and restore wetlands on the Refuges. The GBP continues to contaminate the northernmost six miles of Mud Slough and the reach of the San Joaquin River between Mud Slough and the Merced River. However, as phasedin load reduction goals are achieved by GDA farmers, these effects are expected to be reduced. An essential component of the GBP is a monitoring program that tracks contaminant levels and effects in water, sediment, and biota to ensure that the overall effect of the GBP is not a net deterioration of the ecosystems in the area affected by the GBP. Contaminants of Concern In the aftermath of the deaths and developmental abnormalities of birds at Kesterson Reservoir in the early 1980s, studies definitively traced the cause to selenium in the agricultural drainwater in the reservoir (Suter, 1993). Because of this, and because of the wellknown history of death, teratogenesis, and reproductive impairment caused by selenium in agricultural drainwater elsewhere (reviewed in Skorupa, 1998), the primary contaminant of concern in this monitoring program is selenium. Other inorganic constituents of potential toxicological concern in drainage water include boron, molybdenum, arsenic, chromium (Klasing and Pilch, 1988; SJVDP, 1990a; CVRWQCB, 1998) and mercury. Selenium Ecological Risk Guidelines The assessment of the risks that selenium poses to fish and wildlife can be difficult due to the complex nature of selenium cycling in aquatic ecosystems (Lemly and Smith, 1987). Early assessments developed avian risk thresholds through evaluating bird egg concentrations and relating those to levels of teratogenesis (developmental abnormalities) and reproductive impairment (Skorupa and Ohlendorf, 1991). In 1993, to evaluate the risks of the proposed Grassland Bypass Project on biotic resources in Mud and Salt Sloughs, a set of Ecological Risk Guidelines based on selenium in water, sediment, and residues in several biotic tissues were developed by a subcommittee of the San Luis Drain Re-Use Technical Advisory Committee (CAST, 1994; Engberg, et.al., 1998). These guidelines (as recently modified: Tables 1 and 2) are based on a large number of laboratory and field studies, most of which are summarized in Skorupa et al. (1996) and Lemly (1993). In areas where the potential for selenium exposure to fish and wildlife resources exists, these selenium risk guidelines can be used to trigger appropriate actions by resource managers, regulatory agencies, and dischargers. For the GBP the selenium risk guidelines have been divided into three threshold levels: No Effect, Concern, and Toxicity. In the No Effect range risks to sensitive species are not likely. As new information becomes available it should be evaluated to determine if the No Effect level should be adjusted. Since the potential for selenium exposure exists, periodic monitoring of water and biota is appropriate. Within the Concern range there may be risk to species sensitive to elevated contaminant concentrations in water, sediment, and biota, and should be monitored on a regular basis. Immediate actions to prevent selenium concentrations from increasing should be evaluated and implemented if appropriate. Long-term actions to reduce selenium risks should be developed and implemented. Research on effects on sensitive or listed species may be appropriate. Within the Toxicity range, adverse affects are more likely across a broader range of species, and sensitive or listed species would be at greater risk. These conditions will warrant immediate action to reduce selenium exposure through disruption of pathways, reduction of selenium loads, or other appropriate actions. More detailed monitoring, studies on site-specific effects, and studies of pathways of selenium contamination may be appropriate and necessary. Longterm actions to reduce selenium risks should be developed and implemented. Warmwater Fish The warmwater fish guidelines (Tables 1 and 2) refer to concentrations of selenium in warmwater fish that adversely affect the fish themselves. Practically all the fish routinely sampled by the GBP monitoring program area are warmwater fish. The concern threshold for warmwater fish has been kept at 4 µg/g (all fish data are whole body, dry weight). Experimental data reported in the literature may be interpreted to support a range of thresholds around this value.

121 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 119 In particular, bluegill sunfish dietary exposure data in Cleveland et al. (1993) and Lemly (1993) support warmwater fish concern thresholds ranging from 2.5 to 3.9 µg/g. Bluegill sunfish are warmwater fish that are found in the sloughs in the GBP area. Cleveland et al. (1993) found no adverse effects after 59 days of exposure to a concentration of dietary selenium (nominally 3.3 µg/g wet weight) that resulted in a bluegill tissue concentration of 2.6 µg/g (whole body dry weight). Fifty nine days of exposure to dietary concentrations that resulted in tissue concentrations of 4.3 µg/g (whole body dry weight) caused a significant increase in mortality relative to controls. Therefore the No Observable Effect Concentration (NOEC) is 2.6 µg/g, and the Lowest Observable Effect Concentration (LOEC) is 4.3 µg/g. Following a standard USEPA method (Stephan et al., 1985), the tissue threshold is calculated as the geometric mean of the NOEC and the LOEC. Application of this procedure to these data yields a threshold of 3.3 µg/g. Other data in Cleveland et al. (1993) support a threshold closer to 4 µg/g. After 90 days of dietary exposure bluegill with a tissue selenium concentration of 3.2 µg/g did not exhibit adverse effects that were significantly greater than controls (NOEC), but bluegill with a tissue concentration of 4.7 µg/g experienced significantly increased mortality (LOEC). The corresponding threshold is 3.9 µg/g (geometric mean of 3.2 µg/g and 4.7 µg/g). Analysis of these data (Cleveland et al., 1993: 90 day) using the logit procedure (linear regression using logit-transformed effect data) yields an LC10 of 2.81 µg/g whole body dry weight (Figure 1C). In an experiment reported by Lemly (1993) juvenile bluegill exposed to dietary selenium (5.16 µg/g dry weight) in the form of seleno-l-methionine for 180 days, while being subjected to conditions (cold temperature and short photoperiod) simulating the onset and about 4 months duration of winter, reached whole body selenium concentrations of 5.8 µg/g (dry weight) at 60 days (beginning of full winter: 4 degrees C water temperature) and 7.9 µg/g (dry weight) at 180 days, and suffered 33.8% mortality at 180 days. Controls (diet: 0.82 µg/g dry weight) subject to the same winter-onset conditions reached whole body selenium concentrations of 1.1 µg/g (dry weight) at 60 days (beginning of full winter) and 1.4 µg/g (dry weight) at 180 days, and suffered 2.8% mortality at 180 days. If this 2.8% control mortality is assumed to be due to causes other than selenium, then the NOEC is 1.4 and LOEC (causing 31% mortality) is 7.9 at 180 days. By the standard USEPA method (Stephan et al., 1985), the tissue threshold is then 3.3 µg/g whole body dry weight (geomean of 1.4 and 7.9 µg/g). However, concentrations of selenium at 180 days were magnified by loss of lipid during winter stress (Lemly, 1993; USEPA, 2004). If the concentrations at 60 days are used as an indication of summer-fall concentrations of bluegill that will reach the 180 day concentrations at the end of winter (USEPA, 2004), then the tissue threshold should be 2.5 µg/g (geometric mean of 1.1 and 5.8 µg/g, the whole-body concentrations of the control and exposed treatment groups respectively at 60 days). Considering that these data do not include adverse effects on reproduction, which may occur at lower concentrations, these thresholds (2.5 to 3.9 µg/g whole body dry weight) may not be fully protective of sensitive warmwater fish species. Coldwater Fish Salmonids (salmon and trout), which are known as coldwater fish, are evidently more sensitive to selenium than other freshwater fish such as sunfish and carp, which are known as warmwater fish. This accords with the greater sensitivity of trout and salmon to a wide range of other contaminants (Teather and Parrott 2006.). Application of a biphasic model (Beckon et al. 2008) to a study of juvenile fall run Chinook salmon (Oncorhynchus tshawytscha) from the Merced River Hatchery (Hamilton et al. 1990) indicates that ten percent mortality attributable to selenium (LC10) is associated with a whole body selenium tissue concentration of 1.84 µg/g dry weight (Figure 1D). Deforest et al. (1999) analyzed these data using the alternative probit and logit methods. Both procedures yielded LC10s of 1.7 µg/g (whole body dry weight). These LC10s are in good agreement with 10 percent effect level (EC10) for rainbow trout (Oncorhynchus mykiss), another salmonid species. Analysis of a study (Hilton et al., 1980) of juvenile rainbow trout (average initial weight: 1.28 g) exposed for 140 days to dietary selenium in the form of sodium selenite indicates that a 10 percent reduction in weight (from optimum weight) is associated with a selenium concentration of 2.19 µg/g in trout tissue (whole body dry weight; Figure 1E). These findings are consistent with the more recent study by Vidal et al.(2005) in which larval rainbow trout (24 days old initially) were exposed for 90 days to dietary selenium in the form of seleno-l-methionine. Rainbow trout that had been fed a diet spiked with 4.6 µg/g selenium reached an average tissue concentration of 0.58 µg/g whole body

122 120 GRASSLAND BYPASS PROJECT wet weight (reported), or 2.64 µg/g whole body dry weight (calculated from wet weight using 75.84% moisture USEPA 2004) and weighed an average of 3.54 g. This is significantly less than the average weight of controls (5.17 g, diet: 0.23 µg/g dry weight), which had an average tissue concentration of 0.31 µg/g whole body wet weight, or 1.41 µg/g whole body dry weight. Thus the LOEC and NOEC are 2.64 µg/g and 1.41 µg/g respectively, and the USEPA method of Stephan et al. (1985) yields a tissue threshold of 1.76 µg/g whole body dry weight (geometric mean of LOEC and NOEC). The analyses above focus on growth and mortality. Reproductive impairment may occur at lower selenium concentrations, but too few data are available to do similar analyses of reproductive effects. Therefore, sensitive coldwater fish species may not be fully protected by any of the thresholds derived from these analyses. Although the fish community in the sloughs affected by the GBP principally consists of warmwater species, anadromous coldwater fish migrate through the portion of the San Joaquin River into which these sloughs discharge. A study by Saiki et al. (1991) showed that migrating juvenile coldwater fish (Chinook salmon) in the reach of the San Joaquin River just below the discharge of Mud Slough bioaccumulated selenium to concentrations of about 3 µg/g (whole body dry weight), levels at which substantial mortality could occur (Figure 1D). Vegetation and Invertebrates The guidelines for vegetation (as diet) and invertebrates (as diet) refer to selenium concentrations in plants and invertebrates affecting birds that eat these items. These guidelines are mainly based on experiments in which seleniferous grain or artificial diets spiked with selenomethionine were fed to chickens, quail or ducks resulting in reproductive impairment (Wilber, 1980; Martin, 1988; Heinz, 1996). The Concern threshold for vegetation is 3 µg/g (dry weight) and the Toxicity threshold is 7 µg/g. The invertebrate concern threshold and toxicity threshold are the same as those for vegetation. Water Fish and wildlife are much more sensitive to selenium through dietary exposure from the aquatic food chain than by direct waterborne exposure. Therefore the guidelines for water reflect water concentrations associated with threshold levels of food chain exposure (Hermanutz et al., 1990; Maier and Knight, 1994), rather than concentrations of selenium in water that directly affect fish and wildlife. The concern threshold is 2 μg/l and the toxicity threshold is 5 μg/l. Sediment As with water, the principal risk of sediment to fish and wildlife is via the aquatic food chain. Therefore the sediment guidelines are based on sediment concentrations as predictors of adverse biological effects through the food chain (USFWS, 1990; Van Derveer and Canton, 1997). The concern threshold for sediment (dry weight) is 2 µg/g and the toxicity threshold is 4 µg/g. Bird Eggs Bird eggs are particularly good indicators of selenium contamination in local ecosystems (Heinz, 1996). However, the interpretation of selenium concentrations in bird eggs in the GBP area is complicated by the proximity of contaminated and uncontaminated sites and by the variation in foraging ranges among bird species. Relative to the guidelines originally used for the GBP, the guidelines used here for individual bird eggs have been revised upward based on recent studies of hatchability of ibis, mallard, and stilt eggs (Henny and Herron, 1989; Heinz, 1996; USDI-BOR/ FWS/GS/BIA, 1998). The concern threshold has been raised from 3 to 6 µg/g dry weight, and the toxicity threshold has been raised from 8 to 10 µg/g dry weight. Selenium Ecological Risk Index Several years after the risk guidelines were developed for the GBP, Lemly (1995, 1996) published a risk index designed to provide an estimate of ecosystemlevel effects of selenium. Lemly s assessment procedure sums the effects of selenium on various ecosystem components to yield a characterization of overall hazard to aquatic life. The procedure involves determining an index of toxicity for each component, then adding these indexes together to yield a single index, often known as the Lemly Index. In contrast to the ecological risk guidelines outlined in Tables 1 and 2, the

123 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 121 component indexes of the Lemly Index are based on maximum contaminant concentrations rather than means. Therefore, the Lemly Index is sensitive to brief spikes in contaminant levels, but is unaffected by prevailing contaminant levels. Furthermore, the Lemly Index is strongly dependent on sampling periods and sampling frequency, yet Lemly provided no sampling protocol. For these reasons, there is a need to develop a new protocol and index that replaces Lemly s categorical rating format (low, medium, high) with a direct estimate of the probability of adverse effects (e.g.10%+ probability of reproductive impairment). Despite the weaknesses of the Lemly Index, we continue to use it for comparative purposes as long as it remains the best available overall index of the ecological risk of selenium. METHODS Agency Responsibilities The role of the California Department of Fish and Wildife (CDFW) and the United States Fish and Wildlife Service (USFWS) in this interagency program is to implement the bio-monitoring portion of the Compliance Monitoring Program. The methods used by the CDFW and USFWS are described in the Quality Assurance Project Plan for Use and Operation of the Grassland Bypass Project (USBR 2001). These methods are also based on standard operating procedures described in Standard Operation Procedures for Environmental Contaminant Operations (USFWS, 1995) and standards used by the other agencies participating in the compliance monitoring program. Deviations from the QAPP that have occurred since 1996 will be discussed later in this section. To obtain baseline data for this Project, the USFWS began sampling in March 1992, after the reuse of the SLD was initially proposed by the USBR in The CDFW began sampling in August of USFWS and CDFW sampling plans before the reopening of the SLD and the early drafts of the monitoring plan were mutually influencing. Therefore, methods used by both agencies before the final approval of the QAPP are, except for a few minor differences, identical to the methods ultimately approved by the Data Collection and Reporting Team. The sampling schedule, though, as discussed below, now follows a regular timetable. Matrices Sampled Samples of the biota were collected at each site and analyzed for selenium and boron. Aquatic specimens were collected with hand nets, seine nets and by electro fishing. Mosquitofish (Gambusia affinis), inland silversides (Menidia beryllina), red shiners (Cyprinella lutrensis), fathead minnows (Pimephales promelas), carp (Cyprinus carpio), white catfish (Ameiurus catus), and green sunfish (Lepomis cyanellus) were the principal species of fish collected. Waterboatmen (family: Corixidae), backswimmers (family: Notonectidae), red swamp crayfish (Procambarus clarkii), and Siberian freshwater shrimp (Exopalaemon modestus) were the principal invertebrates collected. Separation of biological samples from unwanted material also collected in the nets was accomplished by using stainless steel or Teflon sieves, and glass (or enamel) pans prerinsed with de-ionized water then native water. To the extent possible, three replicate, composite samples (minimum 5 individuals totaling at least 2 grams for each composite) of each primary species listed above were collected, but other species were also collected. Fish species were analyzed as composite wholebody samples except as noted below. Estimates of a conversion factor for relating selenium concentration in skeletal muscle (M) to wholebody concentrations (WB) range from M=0.6xWB for many freshwater fish (Lemly and Smith, 1987) to M= xWB for bluegills and M= xWB for largemouth bass (Saiki et al., 1991). Between 1992 and 1999, frog tadpoles occasionally collected from Mud Slough and Salt Slough sites were archived. In 1999 these archived samples were analyzed. Additional samples have been collected and analyzed from these sites since The seed heads of wetland plants that provide food for waterfowl were collected along the sloughs in the late summer (August) of each year from the beginning of the Project until This plant material was analyzed for boron as well as selenium. Analysis of plant material for selenium and boron was suspended in Waterfowl and/or shorebird eggs, depending on availability, were collected from areas adjacent to Mud Slough and the SLD in the spring of each year since In addition, in 1992 snowy egret and blackcrowned night heron eggs were collected at East Big Lake, which has served as a reference sampling site for the USFWS. Bird eggs were analyzed individually, and the results are discussed and displayed below as individual concentrations and geometric means.

124 122 GRASSLAND BYPASS PROJECT Graphs of wholebody and avian egg selenium concentrations presented in this report include indications of the threshold concentrations delimiting the risk ranges listed above (Tables 1 and 2). The threshold between the No Effect Zone and the Concern Zone is indicated by a horizontal line of short dashes; the Toxicity threshold is marked on each graph by a horizontal line of long dashes. All biota samples were kept on ice or on dry ice while in the field then kept frozen to zero degrees centigrade during storage and shipment. For all samples, after freeze-drying, homogenization, and nitricperchloric digestion, total selenium was determined until 2014 by hydride generation atomic absorption spectrophotometry, subsequently by fluorometry. Sampling Sites Between 1992 and 1999, biological samples were collected from two sites on Salt Slough, five sites on Mud Slough, two sites in the SLD, two sites on the San Joaquin River, and one reference site that does not receive seleniumcontaminated drainwater (East Big Lake). Beginning in 1995, sampling efforts were concentrated on the seven sites (Figure 1a) identified in the Compliance Monitoring Plan: four sites on Mud Slough (C, D, E, and I), one on Salt Slough (F) and two San Joaquin River sites (G and H). Site C is located upstream of where the SLD discharges into Mud Slough. Site D is located immediately downstream of the discharge point. Site I is a small, seasonally flooded backwater area fed by Mud Slough and is located approximately 1 mile downstream from Site D. In March, 2001, biological sampling in Mud Slough was moved from Site I to a new site (Site I2) about 0.5 km upstream of Site I. The new site has a larger, more persistent backwater area. Site E is located further downstream where Mud Slough crosses State Highway 140. To assess the mitigative effects of drainwater removal from Salt Slough, one sample point, Site F, is located on the San Luis National Wildlife Refuge approximately 2 miles upstream of where State Highway 165 crosses Salt Slough. Site G is located on the San Joaquin River at Fremont Ford, upstream of the Mud Slough confluence, while Site H is located on the San Joaquin River 200 meters upstream of the confluence of the main branch of the Merced River, downstream of the Mud Slough confluence. Sites C, D, F, and I2 are monitored by the USFWS while CDFW monitors Sites E, G, and R. Sampling Times Baseline sampling conducted by the USFWS occurred monthly during the spring and summer of 1992 and then less frequently during 1993 and Baseline sampling by CDFW occurred during the summer and fall of 1993 and then resumed in the spring of Between 1992 and 1995 sampling by either the CDFW or the USFWS occurred at least once every season. Experience and interagency discussions led to the identification of four sampling times based on historic water use and drainage practices and on seasonal use of wetland resources by fish and wildlife. Biota sampling since 1995 has been synchronized to occur during the months of November, March, June, and August. Since 1996, avian eggs have been collected in May and June. Statistical Analysis Student s 2tail ttests (unpaired samples with unequal variances) were used to compare means of concentrations for groups of samples collected at different times at the sampling sites. Selenium Hazard Assessment The protocol proposed by Lemly (1995, 1996) was used to estimate the overall hazard of selenium to the ecosystems affected by the GBP. The implementation of the protocol presented here incorporates data for water from Central Valley Regional Water Quality Control Board and data for sediment from the USBR in addition to biological data collected by the USFWS and CDFW. In accordance with Lemly s protocol, the assessments use the highest (rather than the mean) concentrations of selenium found in each of the ecosystem components (Tables 3 and 4). Data from the biological sampling in November 1996, shortly after GBP initiation, were excluded from the WY 1997 hazard assessments because temporarily extremely high concentrations of selenium in some fish may have been due to those fish having been flushed out of the previously stagnant, evapo-concentrated SLD. Very high levels of selenium in the water associated with storm flows were not excluded because elevated concentrations persisted long enough (especially in February 1998) potentially to affect the ecosystem adversely.

125 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 123 Concentrations of selenium in fish eggs were estimated from wholebody concentrations using the conversion factor (fish egg selenium = fish wholebody selenium x 3.3) recommended in Lemly (1995, 1996). Site E (lower Mud Slough) and the San Joaquin River (SJR) sites (G and H) cannot be rated as to overall hazard of selenium because not all media have been collected to assess these sites. Departures from the Monitoring Plan and Quality Assurance Project Plan To ensure reliable and consistent data, the USFWS and the CDFW followed the procedures specified in the Monitoring Plan and the Quality Assurance Project Plan (QAPP) with the exceptions listed below. External quality assurance samples (QAPP Appendix A, Section 7) were not submitted to analytical labs with GBP biological samples before January of External quality assurance samples are biological materials (e.g. powdered chicken egg, shark liver) with certified concentrations of the analytes of concern (selenium, boron), supplied by third party laboratories. The analyte concentrations in these samples are known to the agencies submitting the samples, but not known to the laboratory doing the analysis. This blind test of laboratory analytical precision supplements the internal quality control procedures of the analytical laboratory. Internal quality control protocols specified in the QAPP (procedural blanks, duplicate samples, and spiked samples) have been followed throughout the history of GBP biological sampling. The USFWS used stainless steel (rather than Teflon) strainers for sorting small fish (QAPP Appendix A, Section 4.7). For some species at some locations it has not been practical at some times to collect the full target minimum numbers of individuals and/or mass per sample that are specified in the Compliance Monitoring Plan (Section ) and the QAPP (Appendix A, Section 4.5). From 1992 through 1997 all biological samples collected by the USFWS (except bird eggs in 1996 and 1997) were analyzed by Environmental Trace Substance Laboratory at the University of Missouri in accordance with the QAPP (Appendix A, Section 6.1). Bird egg samples collected in 1996 and 1997 were analyzed at Trace Element Research Laboratory (TERL) at Texas A & M University, a USFWS contract laboratory. All biological samples collected in 1998 were analyzed at TERL. TERL is subject to the same performance standards as Environmental Trace Substance Laboratory, therefore, the GBP quality assurance objectives (QAPP Table 1) apply to analytical results from TERL. All biological samples beginning in 1999 have been analyzed at the Water Pollution Control Laboratory of the CDFW in Rancho Cordova, California, after this laboratory was screened and approved by the GBP Quality Control Officer. Seine net mesh size was increased from 3/16 inch to 1/4 inch after the first two preproject collections in 1993 from sampling sites E, G, and H (QAPP Appendix A, Section 4.6). This change in sampling gear resulted in significant declines in catch abundance of smaller forage fish without altering diversity of representative assemblages. Data collected from 1993 sampling efforts at these sites were not included in making quantitative spatial or temporal comparisons between sites unless otherwise noted. At sites C, D, I, and F, 1/8 inch mesh seines were used from 1992 through Since 1999, a 3/16 inch mesh bag seine has been used at these sites in place of the 1/8 inch mesh bag seine that was previously used by the USFWS. As discussed earlier, biological sampling in Mud Slough was moved from Site I to Site I2, a new site about 0.5 km upstream with a larger, more permanent backwater area. RESULTS Salt Slough (Site F) Salt Slough is a principal wetland water supply channel from which drainwater has been removed by the GBP. Selenium in fish Concentrations of selenium in Salt Slough fish composite samples declined rapidly during the first year of operation of the GBP. Concentrations then stabilized at levels generally below the concern threshold for warmwater fish (4 µg/g), but continued to trend downward as concentrations of selenium continued to decline gradually since the first year of the project (Figures 2-2E).

126 124 GRASSLAND BYPASS PROJECT During the three-year period , of the 145 samples of fish collected at this site (mostly composite samples), only one sample (a sample of 4 bluegill, average mass 25.7 g: 4.22 µg Se/g) exceeded the concern threshold for warmwater fish (4 µg/g, Table 1). The average selenium concentration in all 145 samples was 2.04 µg/g (geometric mean 1.98 µg/g), well under the 4 µg/g threshold of concern, and significantly lower (p=0.008) than the average selenium concentration in all 85 fish samples collected in the previous two years ( : 2.28 µg/g, geometric mean 2.18 µg/g). In the final year (2014) of this three-year reporting period, selenium concentrations in fish in Salt Slough reached historic lows: the average selenium concentration in the 50 fish samples collected in 2014 was 1.75 µg/g (geometric mean 1.70 µg/g), significantly lower (p= ) than the average selenium concentration in the 95 fish samples collected in the previous two years ( : 2.20 µg/g, geometric mean 2.14 µg/g). Selenium in invertebrates Concentrations of selenium in invertebrates in Salt Slough declined abruptly after the cessation of agricultural drainwater discharges into this slough with the implementation of the Grassland Bypass Project in October Since that initial decline, selenium concentrations in invertebrates as well as ambient water continued to trend downward until about (Figure 2F). Then, during the two-year period of , the mean concentration of selenium in all invertebrate samples (n=19) rose somewhat. The mean (2.18 µg/g, geometric mean 1.97 µg/g) was significantly (p=0.003) above the mean concentration of selenium in all invertebrate samples collected during the previous two years ( : 1.48 µg/g, geometric mean 1.40 µg/g, n=23), and above (p=0.04) the broader average for the previous 14 year period ( (1.76 µg/g, n=136), but still highly significantly (p=4x10-8) below the preproject average (4.37 µg/g, geometric mean 4.15, n=27). The apparent rise in selenium concentrations in invertebrates in Salt Slough in tracked a similar rise in selenium concentrations in the water (Figure 2F), and may have been due in part to the onset of severe, multi-year drought in California. It may also have been partly the result of a seemingly temporary increase in the abundance of Siberian freshwater shrimp relative to red swamp crayfish (Figure 2F). The Siberian freshwater shrimp tend to bioaccumulate selenium to higher levels than those found in red swamp crayfish. In 2014, the mean concentration of selenium in invertebrates in Salt Slough declined again as the surge in numbers of Siberian freshwater shrimp faded and red swamp crayfish reappeared (Figure 2F). The mean concentration in 2014 samples (n=13) was 1.09 µg/g (geometric mean: 0.96 µg/g) significantly lower (p= ) than the mean for the period (2.18 µg/g, geometric mean 1.97 µg/g) and significantly lower (p= ) than the mean for the broader (16-year) period (1.81 µg/g). Five of the 19 composite invertebrate samples collected from Salt Slough in (4 samples of Siberian freshwater shrimp and 1 sample of Asian clams) exceeded the threshold of concern for dietary risk to wildlife that eat aquatic invertebrates (3 µg/g). During the previous four years there had been no such exceedances, and there were no such exceedances in Mud Slough upstream of the San Luis Drain discharge (Site C) This sampling location, about 400 m upstream of the outfall of the SLD, was intended to serve as a reference site, representing the baseline conditions in Mud Slough that would prevail in lower Mud Slough (North) were it not for drainwater discharges into lower Mud Slough due to the Grassland Bypass Project. However, evidence emerged that this site, though upstream from the SLD discharge, is close enough to the discharge point that fish samples at this site are affected by upstream movement of fish from the downstream drainwater. Evidence for this can be seen in the very high concentrations of selenium in mosquitofish and silversides sampled at this site as well as Site D (just downstream of the discharge) in the months immediately after the opening of the Grassland Bypass Project in October 1996 (compare Figures 6A and 6B with Figures 10A and 10B). There is no known reason for such a spike in selenium in fish at this site apart from the hypothesis that some selenium-laden fish moved upstream from the discharge of the San Luis Drain. Selenium in fish In 2014, concentrations in fish rose to levels not seen at this site since immediately following the opening of the San Luis Drain (Figure 3). In the first year (2012) of the three-year reporting period , the average selenium concentration in fish at Site C (3.23 µg/g, geometric mean 2.94 µg/g, n=38) was not significantly different (p=0.51) from the long-term average (3.39 µg/g, n=742), but in 2013, the average (5.31 µg/g, geometric mean

127 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I , n=37) rose significantly (p= ) above that long-term average. In 2014 the average rose still higher (5.95 µg/g, geometric mean 4.23 µg/g, n= 35), but not significantly (p=0.166) higher than the previous year (2013). Selenium concentrations exhibited much greater variance in 2014 (34.7) than in 2013 (8.03), with some fish samples (adult mosquitofish and Mississippi silversides) in November 2014 reaching extremely high concentrations soon after some samples (juvenile mosquitofish and killifish) in August had low concentrations (Figures 3A and 3E). The rise in selenium concentrations in fish in 2014 did not track concentrations in water at this site. However, a close look at the concentrations in individual species indicates that the rise in the average concentration was driven entirely by rising selenium concentrations in just two species: mosquitofish and Mississippi silversides (Figures 3A and 3B). These are exactly the same two species in which selenium concentrations rose sharply at this site in late 1996 through 1997, immediately following the reopening of the San Luis Drain at the commencement of the Grassland Bypass Project. Other species of fish either exhibited no rise in selenium concentrations (minnow family: Figure 3C, rainwater killifish: Figure 3E), or were not caught in our samples (Figure 3D) in 2013 and 2014 (low fish diversity probably due to very low flows at this site caused by severe drought conditions). The seemingly anomalous divergence at this site between selenium concentrations in just two species of fish on one hand, and water on the other hand may be resolved by the following explanation. By August, September, and October of 2014, discharge from the San Luis Drain slowed to a trickle, and intermittently ceased altogether. When substantial discharge resumed in November 2014, conditions may have replicated those at the reopening of the San Luis Drain in 1996, when initial discharges evidently swept fish out of the Drain into Mud Slough, from whence at least some individuals of two species (mosquitofish and Mississippi silversides) moved upstream as far as Site C where they were captured in our seines along with locally resident fish. These migratory individuals had bioaccumulated high concentrations of selenium in the previously stagnant water in the Drain. In November 2014, all composite samples of mosquitofish and Mississippi silversides collected at Site C had concentrations of selenium well above the toxicity threshold of 9 µg/g (Figures 3A and 3B). Selenium in invertebrates Unlike fish, invertebrates at Site C, above the discharge of San Luis Drain, seem to have been uninfluenced by that discharge (Figure 6F). Selenium concentrations provide no evidence that any invertebrates that may have been flushed from the Drain were able to make their way upstream to Site C. That is, there is no evidence of a spike in invertebrate selenium concentrations at this site immediately following the initial discharge of highly seleniferous water from the San Luis Drain in 1996, nor in November 2014 when discharge resumed after drought-induced cessations. Evidently, invertebrates do not swim upstream to the extent exhibited by some fish (Mississippi silversides and adult mosquitofish) here. In 2014, the average selenium concentration in invertebrates collected at Site C (1.07 µg/g, geometric mean 0.88 µg/g, n=15) fell significantly (p=0.025) below the average for the previous year (2013: 1.23 µg/g, geometric mean 1.98 µg/g), and significantly (p= ) below the longer term average from 1998 to 2013 (1.93 µg/g, n=165). This decline in invertebrate selenium concentrations seemed to track a decline in the selenium concentrations in the water at Site C, but it may also have been due in part to a decline in the relative abundance of the Siberian freshwater shrimp, Exopalaemon modestus (Figure 3F), which may not be well adapted to the severe drought conditions prevailing here in This recently-arrived east Asian palaemonid shrimp first appeared in the lower Sacramento River in 2000 (Hieb et al. 2002). By 2003 when it was first encountered in the GBP monitoring program, it was already becoming one of the most common invertebrate species seined at this location in Mud Slough. The propensity of the newly-arrived Siberian freshwater shrimp to bioaccumulate selenium evidently is substantially higher than that of other aquatic arthropods in the area (Figure 3F). From 2003 until 2013, the presence of this species has elevated the average invertebrate selenium concentration at this site. Mud Slough just below San Luis Drain discharge (Site D) This sampling location, about 200 m downstream of the outfall of the SLD, was intended to represent the effects of discharged drainwater on the biota of Mud Slough. However, this site is even closer than the upstream site (Site C) to the point where the San Luis Drain discharges in to Mud Slough. Therefore, evidence that contaminated fish swim upstream to Site C (see above) also suggests that relatively clean fish from above the discharge point swim downstream and are likely to be included among the fish seined at Site D. Consequently, composite samples collected at this site may be effectively diluted by clean fish, and may not represent the full effects of drainwater discharged by the Grassland Bypass Project.

128 126 GRASSLAND BYPASS PROJECT Selenium in fish During the reporting period , as the effects of a historically severe drought set in, the diversity of fish caught at this site was reduced (Figures 4D and 4E), and selenium in some of the surviving fish at this site reached very high concentrations (Figures 4A and 4B), as high as 51.7 µg/g in a composite sample of 250 small Mississippi silversides in August 2014, far above the fish toxicity threshold of 9 µg/g. In the first year of this period (2012), the average selenium concentration in fish (7.04 µg/g, geometric mean 6.53, n=44) was not significantly different (p=0.29) from the long-term average (6.59 µg/g, n=586) for the previous 14 years ( ), but in 2013 the average (11.9 µg/g, geometric mean 9.90, n=33) rose significantly (p= ) above that 14-year average, and in 2014 the average selenium concentration in fish at this site (22.64 µg/g, geometric mean µg/g, n=30) reached a higher level than any previously recorded since monitoring for this project began in This average was very significantly (p= ) higher than the average. Seemingly paradoxically, during this same period, some measurements of selenium in water dropped to levels lower than any measured at this site since the San Luis Drain began discharging into Mud Slough in Three factors may explain this apparently paradoxical mismatch between selenium in the fish and in the ambient water: (1) it is well-established that selenium is assimilated more efficiently in lentic (static water) conditions than in lotic (flowing water) conditions, and as the drought has worsened in California, flows in Grassland sloughs (and at Site D in particular) have slowed dramatically, approaching lentic conditions conducive to enhanced bioaccumulation of selenium; (2) flows of relatively low-selenium water from upstream Mud Slough have continued (albeit at low rates of flow) while discharges of seleniferous water from the San Luis Drain have been intermittently reduced to zero or near zero flows; thus sporadically the water at this site was unusually low in selenium because it largely or entirely comprised flows from upstream Mud Slough; (3) at times of discharge from the San Luis Drain, two species (Mississippi silversides and mosquitofish), may have moved from the previously near-stagnant waters in the Drain (high concentrations of selenium and highly conducive to bioaccumulation) into Mud Slough, swimming upstream to Site C as well as downstream to be included in our fish samples at Site D, and possibly as far downstream as Site I2. This latter suggestion is supported by the fact that the rise in average selenium in fish at this site in 2013 and 2014 was mainly due to dramatic increases in selenium in those two species (Figures 4A and 4B). Selenium in other common forage fish (red shiners and fathead minnows) rose to a much lesser extent (Figure 4C). Selenium in invertebrates Invertebrates have been relatively difficult to collect in numbers at Site D since the SLD began discharging drainwater into Mud Slough. The slough in this reach is generally steep-sided, relatively deep, and fast-flowing. Scouring minimizes streamside emergent vegetation, reducing food and cover for invertebrates. While loads of selenium discharged into Mud Slough from the SLD have declined substantially since the beginning of the GBP (see Chapter 2 of this report), and concentrations of selenium in water at this site have trended downward somewhat (Figure 4 and see Chapter 4 of this and previous reports), selenium concentrations in invertebrates at this site have not tracked the decline in ambient selenium (Figure 4F). Rather, averages of selenium concentrations in invertebrates have risen significantly (p=0.02) since the first two years of operation of the Grassland Bypass Project ( average 2.6 µg/g, geometric mean 2.2, n=11; average 4.9 µg/g, geometric mean 4.0, n=12). This may be due in part to the invasion of the Siberian freshwater shrimp. The explosion in numbers of this shrimp seems to have occurred later and to a lesser extent at this site than upstream at Site C (see above). A single Siberian freshwater shrimp was collected at this site in March 2003 when 13 were collected at Site C, but not until November 2003 was this species collected here in sufficient numbers to be analyzed for selenium. As elsewhere in the Grassland area, Siberian freshwater shrimp here evidently have been bioaccumulating selenium to higher levels than other aquatic arthropods (Figure 4F). In , the average selenium concentration in invertebrates (5.26 µg/g, geometric mean 3.87, n=11) was not significantly different (p=0.89, 2-tail t-test) from that of the previous two years ( : 5.04 µg/g, geometric mean 4.54, n=9), and not significantly different (p=0.46, 2-tail t-test) from the longer-term average for the previous 14 years ( : 4.18 µg/g, n=82). All these averages exceeded the threshold of concern (3 µg/g) for dietary exposure to fish and wildlife. In 2014, the average selenium concentration in invertebrates reached a higher level (9.53 µg/g, geometric mean 7.30 µg/g, n=10) than any yearly average measured at this site since monitoring of invertebrates began here in The 2014 average was significantly (p=0.052) higher than the average for the previous two years ( ) and significantly (p=0.015) higher than the average for ). This rise in average invertebrate selenium occurred despite the fact that after March, 2014, no Siberian freshwater shrimp were caught in seining at

129 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 127 this site. Since Siberian shrimp first appeared at this site in March 2003, relatively high concentrations of selenium in this exotic species had consistently raised the average invertebrate selenium concentration. In the latter part of 2014, it was an unprecedented rise in selenium in waterboatmen, rather than Siberian freshwater shrimp that drove the rise in average invertebrate concentrations (Figure 4F). This rise in invertebrate selenium concentrations occurred as selenium in ambient water at this site intermittently reached historic lows. Possible explanations for this mismatch may be similar to those suggested above for a similar phenomenon in fish at this site, those explanations including near lentic conditions conducive to enhanced bioaccumulation, and the possibility that some aquatic organisms were flushed into this site from the San Luis Drain after having bioaccumulated selenium in even more lentic and evapoconcentrated conditions. Waterboatmen would be the most likely invertebrate candidate for such passive migration. Mud Slough backwater 1.5 km below San Luis Drain discharge (Site I/I2) Site I2 is intended to be a better representation of the adverse effects of bioaccumulative drainwater contaminants than Site D, because there is a seasonal backwater at Site I2. Stagnant conditions and evapoconcentration in such backwaters increase selenium assimilation into aquatic food chains. In addition, this site is located farther downstream from the cleaner reach of Mud Slough upstream of the outfall of the SLD. Therefore, the concentrations of contaminants in mobile aquatic organisms collected here are less likely to be diluted effectively by feeding in nearby cleaner water. Collections of biota at this site comprise seining in the main channel of Mud Slough as well as in the adjacent backwater. Usually the backwater is dry or nearly dry in summer and early autumn (during June and August sampling events); at these times Site I2 biota are collected solely from the main channel. Therefore, collections at this site do not fully represent the worst-case scenario of bioaccumulation in backwaters. Selenium in fish Selenium concentrations in fish at this site have been significantly (p=3.6x10-22) higher than concentrations at Site D, just below the drain outfall ( Site I/I2 average 8.22 µg/g, n=636; Site D average 6.59, n=586). In the first year (2012) of this reporting period, the average selenium concentration in fish at this site (7.51 µg/g, geometric mean 7.04 µg/g, n=34) was not significantly different (p=0.12) from the longer-term average (8.22 µg/g, n=636). As at Site D, concentrations of selenium in fish at Site I2 rose in 2013 and 2014, but not to the same extent as at Site D. The average in 2013 (11.25 µg/g, geometric mean 9.80, n=38) was significantly (p= ) higher than the average. The average in 2014 was even higher (16.9 µg/g, geometric mean 14.8 u/g, n=38), very significantly higher (p=5.3x10-9) than the average, but not as high as the average for the same period upstream at Site D (22.64 µg/g). As at Site D, the rise in average selenium concentrations in fish in 2013 and 2014 was driven by sharp rises in just two species, Mississippi silversides and mosquitofish (Figures 5A and 5B); selenium in other small forage fish did not rise to the same extent (Figure 5C). This suggests that the above-proposed reasons for the rise in selenium in fish at Site D may also apply to the similar but lesser rise at Site I2, the influence of fish migrating from the Drain being less because of the greater distance from the Drain outfall. Selenium in invertebrates Selenium concentrations in invertebrates at this site have not declined as selenium loads and concentrations in the water of Mud Slough have trended downward since the start of the GBP (Figure 5F). This appears to be due in large measure to the presence since 2004 of the exotic Siberian freshwater shrimp, which bioaccumulates selenium to a greater extent than other invertebrates. The average selenium concentration in invertebrates in (4.33 µg/g, geometric mean 4.09, n=12) was not significantly different (p=0. 15) from the average for the previous two-year period, (5.38 µg/g, geometric mean 4.75, n=24), and not significantly different (p=0.08) from the longer-term average for the previous 14 years ( : 5.20 µg/g, n=141). In 2014, the average selenium concentration in invertebrates at this site (9.17 µg/g, geometric mean 7.80 µg/g, n=7) rose significantly (p=0.025) above the previous year (2013: 4.16 µg/g, geometric mean 4.25, n=7). The increase in 2014 relative to the long-term ( ) average was significant (p=0.052) but not as pronounced as the increase in selenium in fish (compare Figures 5 and 5F). This suggest that invertebrates (probably in contrast to fish; see above paragraph) underwent little, if any, migration from the Drain to this site. Of the 12 invertebrate samples collected at this site in , nine had selenium concentrations above the threshold of concern for birds that might forage on these invertebrates (3 µg/g) but none had a selenium concentration above the dietary toxicity threshold of 7 µg/g. In 2014, all of the invertebrate samples collected at this site had

130 128 GRASSLAND BYPASS PROJECT selenium concentrations above the dietary threshold of concern for birds; three of them (Siberian freshwater shrimp, waterboatmen, and water beetles) had concentrations above the dietary toxicity threshold for birds. Selenium in amphibians Selenium concentrations (Figure 6) in bullfrog tadpoles (Rana catesbeiana) have followed approximately the same trends exhibited by fish (Figures 2-5). At sites from which drainwater was removed by the Grassland Bypass Project (Sites C and F), the average concentration in (1.94 µg/g, n=4) was not significantly (p=0.84) different from the average in the previous two-year period, (2.01 µg/g, n=7) but significantly (p=0.002) lower than the longer term average over the previous 14 years, (2.82 µg/g, n=50). No tadpoles were collected at either of these sites in At the Mud Slough sites downstream of the drainwater discharge (Sites D and I) no tadpoles were found during the entire reporting period , in line with a general decline in diversity of aquatic life probably associated with the onset of severe draught in this region. Selenium in bird eggs 35 bird eggs were collected in the Grassland area in (Figure 7). Two of these eggs exceeded the concern threshold for avian eggs (6 µg/g; see Table 1). Both were collected along the San Luis Drain: one from the nest of a killdeer, Charadrius vociferus (7.41 µg/g, collected May 8, 2012), and the other from the nest of a cliff swallow Hirundo fulva (6.03 µg/g, collected April 30, 2013). During this reporting period ( ) the selenium concentrations in eggs collected in the vicinity of the San Luis Drain and Mud Slough below the drain discharge (average 3.23 µg/g, geometric mean 2.79, n=20) were significantly (p=0.0024) higher than the concentrations in the general vicinity of Salt Slough (average 1.86 µg/g, geometric mean 1.72, n=15). Aquatic Hazard Assessment of Selenium To provide an estimate of ecosystemlevel effects of selenium, Lemly (1995, 1996) developed an aquatic hazard assessment procedure that sums the effects of selenium on various ecosystem components to yield a single characterization of overall hazard to aquatic life. Because the Lemly index is based on maximum concentrations, it is strongly influenced by data outliers. However, it remains the best selenium hazard index available at this time. Lemly s procedure applied to Mud Slough downstream of the SLD outfall indicated that the hazard to aquatic life continued to be high in 2012, 2013, and 2014 (Table 3a). In the Salt Slough area, the Lemly index remained low throughout this reporting period ( ; Table 3b). A Lemly index was not determined for San Joaquin River sites due to lack of sufficient sample of invertebrates and because bird eggs, one component of the index, were not sampled there. ACKNOWLEDGMENTS We greatly appreciate the assistance provided in the field by Amber Aguilera, Kevin Aceituno, Jerry Bielfeldt,, and Caroline Marn from the Sacramento Fish and Wildlife Service Office, and by Kate Guerena and Tim Keldsen from the San Luis National Wildlife Refuge Complex. Leila Horibata and Micheale Easley from the Bureau of Reclamation also kindly assisted us in the field. REFERENCES Beckon, W. N., M. Dunne, J. D. Henderson, J. P. Skorupa, S. E. Schwarzbach, and T. C. Maurer Biological effects of the reopening of the San Luis Drain to carry subsurface irrigation drainwater. Chapter in Grassland Bypass Project Annual Report October 1, 1996 through September 30, U. S. Bureau of Reclamation, Sacramento, California. Beckon, W. N., A. Gordus, and M. C. S. Eacock Biological Effects. Chapter 7 in Grassland Bypass Project Annual Report San Francisco Estuary Institute, Oakland, California. Brandes, P.L. and McLain, J.S. Juvenile chinook salmon abundance, distribution, and survival in the SacramentoSan Joaquin Estuary. Fishery Bulletin, 179 (in press). Brown, L.R., and P.B. Moyle Native fishes of the San Joaquin drainage: status of a remnant fauna and its habitats. Pages 8998 in D.

131 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 129 F. Williams, T.A. Rado, and S.Bryde, eds. Proceedings of the Conference on Endangered and Sensitive Species of the San Joaquin Valley, California. California Energy Commission, Sacramento, CA. CAST Risk and benefits of selenium in agriculture. Council for Agricultural Science and Technology, Ames, Iowa. Issue Paper No. 3. Caywood, M.L Contributions to the life history of the splittail Pogonichthys macrolepidotus (Ayres). M.S. Thesis. California State University, Sacramento.77pp. CEPA (California Environmental Protection Agency Regional Water Quality Control Board Central Valley Region) Agricultural Drainage Contribution to Water Quality in the Grassland Watershed of Western Merced County, California: October September 1998 (Water Year 1998). CH2M HILL Kesterson Reservoir 1999 Biological Monitoring. Prepared for U. S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, California CRWQCBCVR (California Regional Water Quality Control Board, Central Valley Region) Waste Discharge Requirements for San Luis and Delta-Mendota Water Authority and United States Department of the Interior Bureau of Reclamation Grassland Bypass Channel Project, Order No , adopted July 24, Cleveland, Laverne, E. E. Little, D. R.Buckler, and R. H. Weidmeyer Toxicity and bioaccumulation of waterborne and dietary selenium in juvenile bluegill (Lepomis macrochirus). Aquatic Toxicology 27: DeForest, David K., K. V. Brix, and William J. Adams Critical review of proposed residue-based selenium toxicity thresholds for freshwater fish. Human and Ecological Risk Assessment 5: Entrix, Inc Quality Assurance Project Plan for the Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project (Final Draft). Prepared for the U.S. Bureau of Reclamation, Sacramento, California. Engberg, A., D.W. Westcot, M. Delamore, and D.D. Holz Federal and State Perspectives on Regulation and Remediation of Irrigation- Induced Selenium Problems. In Environmental Chemistry of Selenium. W.T. Frankenberger, Jr. and R.A. Engberg, eds. Marcel Dekker, Inc., NY. Fairbrother, A., K. V. Brix, J. E. Toll, S. McKay, W. J. Adams Egg selenium concentrations as predictors of avian toxicity. Human and Ecological Risk Assessment 5: Gersich, F. M Evaluation of a static renewal chronic toxicity test method for Daphnia magna Straus using boric acid. Environ. Toxicol. Chem. 3: Hamilton, Steven J., K. J. Buhl, N. L. Faerber, R. H. Wiedmeyer, and F. A. Bullard Toxicity of organic selenium in the diet to chinook salmon. Environ. Toxicol. Chem. 9: Hieb K, Greiner T, Slater S San Francisco Bay species 2002 status and trends report. IEP Newsletter 16: Heinz, Gary H Selenium in birds. Pages in: W. N. Beyer, G. H. Heinz, and A. W. Redmon, eds., Interpreting Environmental Contaminants in Animal Tissues. Lewis Publishers, Boca Raton, Florida. Heinz, Gary H., D. J. Hoffman, and L. G. Gold Impaired reproduction of mallards fed an organic form of selenium. J. Wildl. Manage. 53: Henny, C. J., and G. B. Herron DDE, selenium, mercury, and white-faced ibis reproduction at Carson Lake, Nevada. J. Wildl. Manage. 53: Hermanutz, R. O., K. N. Allen, T. H. Roush, and S. F. Hedtke Selenium effects on bluegills (Lepomis macrochirus) in outdoor experimental streams [abs.]. In: Environmental contaminants and their effects on biota of the northern Great Plains. Symposium, March 20-22, 1990, Bismarck, North Dakota. Wildlife Society, North Dakota Chapter, Bismarck, North Dakota. Hilton J.W., P. V. Hodson, and S. J. Slinger The requirement and toxicity of selenium in rainbow trout (Salmo gairdneri). J Nutr 110: Kjelson, M.A., Raquel, P.F., and Fisher, F.W Life history of fallrun juvenile chinook salmon, Oncorhynchus tshawystcha, in the SacramentoSan Joaquin Estuary, California. Pages in V.S. Kennedy, editor. Estuarine Comparisons. New York (NY): Academic Press. Klasing, Susan A., and S. M. Pilch Agricultural Drainage Water Contamination in the San Joaquin Valley: a Public Health Perspective for Selenium, Boron, and Molybdenum. Lemly, A.D Guidelines for Evaluating Selenium Data from Aquatic Monitoring and Assessment Studies. Environ. Monitor. Assess., 28:83B100. Lemly, A.D A Protocol for Aquatic Hazard Assessment of Selenium. Ecotoxicology Environ. Safety., 32:280B288 Lemly, A.D Assessing the toxic threat of selenium to fish and aquatic birds. Environ. Monitor. Assess., 43:19B35.

132 130 GRASSLAND BYPASS PROJECT Lemly, A.D. and G.J. Smith Aquatic Cycling of Selenium: Implications for Fish and Wildlife. Fish and Wildlife Leaflet 12, U.S. Department of the Interior, Fish and Wildlife Service, Washington, DC. Lewis, M. A., and L. C. Valentine Acute and chronic toxicities of boric acid to Daphnia magna Straus. Bull. Environ. Contam. Toxicol. 27: Maier, K. J., and A. W. Knight Ecotoxicology of selenium in freshwater systems. Rev. Environ. Contam. Toxicol., 134: Martin, P. F The toxic and teratogenic effects of selenium and boron on avian reproduction. M. S. Thesis, University of California, Davis, California. McGinnis, S.M Freshwater Fishes of California. University of California Press, Berkeley, California. Meng, L. and Moyle, P.B Status of splittail in the SacramentoSan Joaquin Estuary. Trans. Amer. Fish Soc. 124: Moyle, P.B Inland Fishes of California. University of California Press, Berkeley, California. Moyle, P.B., L.R. Brown, and B. Herbold Final report on development and preliminary tests of indices of biotic integrity for California. Final report to the U.S. Environmental Protection Agency, Environmental Research Laboratory, Corvallis, OR. NIWQP (U.S. Department of Interior, National Irrigation Water Quality Program) Guidelines for Data Interpretation for Selected Constituents in Biota, Water, and Sediment. National Irrigation Water Quality Program Report No. 3, November OEHHA (Office of Environmental Health Hazard Assessment) California sport fish consumption advisories. OEHHA, Sacramento, California. Poston H. A., G. F. Combs, and L. Leibovitz Vitamin E and selenium interrelations in the diet of Atlantic salmon (Salmo salar): gross, histological and biochemical signs. Journal of Nutrition 106: Saiki, M. K An Ecological Assessment of the Grassland Bypass Project on Fishes Inhabiting the Grassland Water District, California. Final Report, prepared for U. S. Fish and Wildlife Service, Sacramento, CA. Saiki, M. K Concentrations of selenium in aquatic foodchain organisms and fish exposed to agricultural tile drainage water. Pages 2533 in Selenium and Agricultural Drainage: Implication for San Francisco Bay and the California Environmental (Selenium II). The Bay Institute of San Francisco, Tiburon, California. Saiki, M. K., M. R. Jennings and S. J. Hamilton Preliminary Assessment of the Effects of Selenium in Agricultural Drainage on Fish in the San Joaquin Valley. In The Economics and Management of Water and Drainage in Agriculture, A. Dinar and D. Ziberman, eds. Kluwer Academic Publishers, Boston, MA. SJVDP (San Joaquin Valley Drainage Program). 1990a. A Management Plan for Agricultural Subsurface Drainage and Related Problems on the Westside San Joaquin Valley. U. S. Department of the Interior and California Resources Agency. Final Report, September SJVDP (San Joaquin Valley Drainage Program). 1990b. Fish and Wildlife Resources and Agricultural Drainage in the San Joaquin Valley. San Joaquin Valley Drainage Program, Sacramento, California. Skorupa, P Selenium Poisoning of Fish and Wildlife in Nature: Lessons from Twelve Real-World Examples. In Environmental Chemistry of Selenium. W. T. Frankenberger, Jr. and R. A. Engberg, eds. Marcel Dekker, Inc., NY. Skorupa, J. P., and H. M. Ohlendorf Contaminants in drainage water and avian risk thresholds. Chapter 18 in The Economics and Management of Water and Drainage in Agriculture. A. Dinar and D. Zilberman eds. Kluwer Academic Publishers. Skorupa, J. P., S.P. Morman, and J. S. Sefchick-Edwards Guidelines for Interpreting Selenium Exposures of Biota Associated with Non-marine Aquatic Habitats. Prepared for the Department of Interior, National Irrigation Water Quality Program by the Sacramento Field Office of the U.S. Fish and Wildlife Service. March pp. Smith, G. J. and V. P. Anders Toxic effects of boron on mallard reproduction. Environ. Toxicol. Chem. 8: Stanley, T. R., Jr., G. J. Smith, D. J. Hoffman, G. H. Heinz, and R. Rosscoe Effects of Boron and selenium on mallard reproduction and duckling growth and survival. Environ. Toxicol. Chem. 16: Stephan, C. E., D. I. Mount, D. J. Hansen, J. H. Gentile, G. A. Chapman and W. A. Brungs Guidelines for deriving numerical national water quality criteria for the protection of aquatic organisms and their uses. National Technical Information Service No. PB USEPA, Washington, D. C. Suter, G. W Retrospective Risk Assessment. Chapter 10 in Ecological Risk Assessment. G. Suter, ed. Lewis Publishers, Boca Raton, FL. Teather K, Parrott J Assessing the chemical sensitivity of freshwater fish commonly used in toxicological studies. Water Qual Res J Canada 41: U.S. Bureau of Reclamation Record of Decision. Grassland Bypass Project. U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento CA.

133 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 131 U.S. Bureau of Reclamation and the San Luis and Delta-Mendota Water Authority Agreement for Use of the San Luis Drain. Agreement No W1319. November 3, U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service, San Luis & Delta-Mendota Water Authority, and U.S. Environmental Protection Agency Consensus Letter to Karl Longley, Chairman, Central Valley Regional Water Quality Control Board. Subject: Basin Plan Amendment for the San Joaquin River. November 3, USEPA (United States Environmental Protection Agency) Draft Aquatic Life Water Quality Criteria for Selenium EPA- 822-D USFWS (U.S. Fish and Wildlife Service) Agricultural irrigation drainwater studies. Final Report to the San Joaquin Valley Drainage Program. U. S. Fish and Wildlife Service, Patuxent Wildlife Research Center, Laurel, Maryland. USFWS (U.S. Fish and Wildlife Service) Standard Operation Procedures for Environmental Contaminant Operations, Vols. I - IX. Quality Assurance and Control Program, U.S. Fish and Wildlife Service, Division of Environmental Contaminants, Quality Assurance Task Force. Washington DC. Van Derveer, W. D., and S. Canton Selenium sediment toxicity thresholds and derivation of water quality criteria for freshwater biota of western streams. Environ. Toxicol. Chem. 16: Vidal, D., S. M. Bay, and D. Schlenk Effects of dietary selenomethionine on larval rainbow trout (Oncorhynchus mykiss). Arch Environ Contam Toxicol 49: Wilber, C. G Toxicology of selenium: A review. Clin. Toxicol. 17: Tables Table 1. Recommended Ecological Risk Guidelines for Selenium Concentrations. Table 2. Recommended Ecological Risk Guidelines for Boron Concentrations. Table 3a. Aquatic Hazard Assessment of Selenium in Mud Slough below San Luis Drain (Lemly Index). Table 3b. Aquatic Hazard Assessment of Selenium in Salt Slough (Lemly Index). Table 4a. Maximum selenium concentration data used for the Lemly Index (Table 4) for Calendar Year 2012 Table 4b. Maximum selenium concentration data used for the Lemly Index (Table 4) for Calendar Year 2013 Table 4c. Maximum selenium concentration data used for the Lemly Index (Table 4) for Calendar Year 2014 Figures Figure 1a. Map of the Grassland Bypass Project Figure 1b. Numbers of Siberian freshwater shrimp collected at sites in Salt Slough (Site F) and Mud Slough upstream (Site C) Figure 1c. Relationship between survival of bluegill (logit-transformed) and concentration of selenium in their tissues Figure 1d. Relationship between survival of juvenile salmon and concentration of selenium in their tissues after 90 days Figure 1e. Relationship between growth of juvenile rainbow trout and concentration of selenium in their tissue Figure 2. Selenium in all fish and water collected in Salt Slough (Site F). Each dot represents a composite sample. Figure 2b. Selenium in Mississippi silversides in Salt Slough (Site F). Figure 2c. Selenium in minnows in Salt Slough (Site F). Figure 2d. Selenium in sunfish and bass in Salt Slough (Site F) Figure 2e. Selenium in various fish in Salt Slough (Site F) Figure 2f Selenium in invertebrates and water in Salt Slough (Site F) Figure 3. Selenium in all fish and water samples in Mud Slough above the San Luis Drain discharge (Site C). Figure 3a. Selenium in mosquitofish in Mud Slough above the San Luis Drain discharge (Site C). Figure 3b. Selenium in Mississippi silversides in Mud Slough above the San Luis Drain discharge (Site C). Figure 3c. Selenium in minnows in Mud Slough above the San Luis Drain discharge (Site C).

134 132 GRASSLAND BYPASS PROJECT Figure 3d. Selenium in sunfish and bass in Mud Slough above the San Luis Drain discharge (Site C). Figure 3e. Selenium in various fish in Mud Slough above the San Luis Drain discharge (Site C). Figure 3f. Selenium in invertebrates in Mud Slough above the San Luis Drain discharge (Site C). Figure 4. Selenium in all fish and water samples in Mud Slough below the San Luis Drain discharge (Site D). Figure 4a. Selenium in mosquitofish in Mud Slough below the San Luis Drain discharge (Site D). Figure 4b. Selenium in Mississippi silversides in Mud Slough below the San Luis Drain discharge (Site D). Figure 4c. Selenium in minnows in Mud Slough below the San Luis Drain discharge (Site D). Figure 4d. Selenium in sunfish and bass in Mud Slough below the San Luis Drain discharge (Site D). Figure 4e. Selenium in various fish in Mud Slough below the San Luis Drain discharge (Site D). Figure 4f. Selenium in invertebrates and water in Mud Slough below the San Luis Drain discharge (Site D). Figure 5. Selenium in all fish samples in a Mud Slough backwater below the Drain discharge (Sites I and I2) and in water at Site D, just below the Drain discharge. Figure 5a. Selenium in mosquitofish in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 5b. Selenium in Mississippi silversides in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 5c. Selenium in minnows in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 5d. Selenium in sunfish and bass in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 5e. Selenium in various fish in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 5f. Selenium in invertebrates in a Mud Slough backwater below the Drain discharge (Sites I and I2). Figure 6. Selenium in frog tadpoles at all sites. Figure 7. Selenium in all bird eggs at all sites.

135 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 133 TABLE 1. RECOMMENDED ECOLOGICAL RISK GUIDELINES FOR SELENIUM CONCENTRATIONS. MEDIUM EFFECTS ON UNITS NO EFFECT CONCERN TOXICITY Water (total recoverable selenium) fish and bird reproduction μg/l < > 5 Sediment fish and bird reproduction µg/g (dry weight) < > 4 Invertebrates (as diet) bird reproduction µg/g (dry weight) < > 7 Warmwater Fish (whole body) fish growth/condition/survival µg/g (dry weight) < > 9 Avian egg egg hatchability µg/g (dry weight) < > 10 (via foodchain) Vegetation (as diet) bird reproduction µg/g (dry weight) < > 7 Notes: 1. These guidelines, except those for avian eggs, are intended to be population based. Thus, trends in means over time should be evaluated. Guidelines for avian eggs are based on individual level response thresholds (e.g., Heinz, 1996; Skorupa, 1998) 2. A tiered approach is suggested with whole body fish being the most meaningful in assessment of ecological risk in a flowing system. 3. The warmwater fish (whole body) concern threshold is based on adverse effects on the survival of juvenile bluegill sunfish experimentally fed selenium enriched diets for 90 days (Cleveland et al., 1993). It is the geometric mean of the "no observable effect level" and the "lowest observable effect level." 4. The toxicity threshold for warmwater fish (whole body) is the concentration at which 10% of juvenile fish are killed (DeForest et al., 1999). 5. The guidelines for vegetation and invertebrates are based on dietary effects on reproduction in chickens, quail and ducks (Wilber, 1980; Martin, 1988; Heinz, 1996). 6. If invertebrate selenium concentrations exceed 6 mg/kg then avian eggs should be monitored (Heinz et al., 1989; Stanley et al., 1996). TABLE 2. RECOMMENDED ECOLOGICAL RISK GUIDELINES FOR BORON CONCENTRATIONS. MEDIUM EFFECTS ON UNITS NO EFFECT CONCERN TOXICITY Water fish (catfish and trout embryos) mg/l < > 25 Water invertebrates (Daphnia) mg/l < > 13 Water vegetation (crops and aquatic plants) mg/l < > 10 Waterfowl diet duckling growth µg/g (dry weight) > 30 Waterfowl egg embryo mortality µg/g (dry weight) <1 > 10 >30 Notes: 1. Water guidelines for invertebrates are based on the "no observed adverse effects level" and "lowest observed adverse effects level" for Daphnia magna (Lewis and Valentine 1981; Gersich 1984). 2. Waterfowl diet guidelines are based on mallard ducks (Smith and Anders 1989). 3. The waterfowl egg no effect level is based on poultry data from Romanoff and Romanoff (1949) and San Joaquin Valley field data for reference sites (R. L. Hothem and Welsh; J. P. Skorupa et al.). 4. The waterfowl egg concern and toxicity thresholds are based on Smith and Anders (1989), Stanley et al. (1996), and the "order-of-magnitude rule of thumb" (toxicity at about 10 times background concentrations). 5. The US Environmental Protection Agency's suggested no adverse response level for drinking water is 0.6 mg/l.

136 Lemly Aq Maximum Selenium concentration Lemly Aquatic hazard Hazard Scale Maximum Selenium concentration Units 134 BEFORE PROJECT Sept WY19 Water µg/l 19 high 5 80 h Sediment µg/g 0.4 none n GRASSLAND BYPASS PROJECT TABLE 3a. AQUATIC HAZARD ASSESSMENT OF SELENIUM IN MUD SLOUGH BELOW SAN LUIS DRAIN (LEMLY INDEX). Invertebrates µg/g 1.6 none Fish eggs µg/g 14.2 moderate h Bird Lemly eggs Aquatic hazard Hazard µg/g Scale Maximum Selenium 3.1 concentration Lemly minimal Aquatic hazard Hazard 2 Scale 4.4 m TOTAL HAZARD SCORE Moderate 13 H Maximum Selenium concentration Lemly Aquatic hazard Hazard Scale Maximum Selenium concentration Lemly Aquatic hazard Hazard Scale Maximum Selenium concentration Units WY20 BEFORE PROJECT GRASSLAND BYPASS PROJECT Phase I GRASSLAND BYPASS PROJECT Phase I Sept WY1997 WY1998 WY1999 WY2000 Water µg/l 19 high 5 80 high high high 5 Water µg/l 66 high 5 51 h Sediment µg/g 4.4 high mo Invertebrates µg/g 15.3 high h Fish eggs µg/g 46.5 high h Sediment µg/g 0.4 none none low high 5 Invertebrates µg/g 1.6 none low high high 5 Fish eggs µg/g 14.2 moderate high high high 5 Bird eggs µg/g 3.1 minimal minimal low low 3 Bird eggs µg/g 5.1 low TOTAL HAZARD SCORE Moderate 13 High 16 High 21 High 23 TOTAL HAZARD SCORE High 23 H GRASSLAND BYPASS PROJECT Phase I GRASSLAND BYPASS PROJECT Phase II Calendar Year 2003 October 1, December 31, 2002 WY2001 WY2000 Water µg/l 66 high 5 51 high high high 5 Calendar Year 2004 Calendar Y Sediment µg/g 4.4 high moderate high high 5 Water µg/l 48.9 high h Sediment µg/g 7.5 high h Invertebrates µg/g high h Fish eggs µg/g 54.6 high h Invertebrates µg/g 15.3 high high high high 5 Fish eggs µg/g 46.5 high high high high 5 Bird eggs µg/g 5.1 low low minimal low 3 TOTAL HAZARD SCORE High 23 High 22 High 22 High 23 Bird eggs µg/g 4.74 minimal TOTAL HAZARD SCORE High 22 H GRASSLAND BYPASS PROJECT Phase II GRASSLAND BYPASS PROJECT Phase II Calendar Year 2004 Calendar Year 2005 Calendar Year 2006 Calendar Year 2007 Calendar Year 2008 Calendar Y Water µg/l 48.9 high high high high 5 Water µg/l 51.0 Sediment µg/g 7.5 high high high high high h 5 Sediment µg/g 1.5 low Invertebrates µg/g high high high high 5 Invertebrates µg/g 9 high h Fish eggs µg/g 54.6 high high high high 5 Fish eggs µg/g 53.8 high h Bird eggs µg/g 4.74 minimal low low minimal 2 Bird eggs µg/g 9.7 low m TOTAL HAZARD SCORE High 22 High 23 High 23 High 22 TOTAL HAZARD SCORE High 21 H GRASSLAND BYPASS PROJECT Phase II GRASSLAND BYPASS PROJECT PHASE III GRASSLAND BYPASS Calendar Year 2008 Calendar Year 2009 Calendar Year 2010 Calendar Year 2011 Calendar Year 2012 Calendar Y Water µg/l 51.0 high high high 5 25 high 5 Water µg/l 23.0 high 5 14 h Sediment µg/g 1 minimal n Invertebrates µg/g 6.3 high h Fish eggs µg/g 44.2 high h Bird eggs µg/g 8.1 low m TOTAL HAZARD SCORE High 20 H Sediment µg/g 1.5 low low high high 5 Invertebrates µg/g 9 high high 5 14 high high 5 Fish eggs µg/g 53.8 high high high high 5 Bird eggs µg/g 9.7 low minimal low low 3 TOTAL HAZARD SCORE High 21 High 20 High 23 High 23 GRASSLAND BYPASS PROJECT PHASE III Calendar Year 2012 Calendar Year 2013 Calendar Year 2014 Hazard Scale Water µg/l 23.0 high 5 14 high high 5 Sediment µg/g 1 minimal none none Hazard Scale: 1 high 5 Invertebrates µg/g 6.3 high high high 5 moderate 4 Fish eggs µg/g 44.2 high high high 5 low 3 Bird eggs µg/g 8.1 low minimal 2 6 low 3 minimal 2 TOTAL HAZARD SCORE High 20 High 18 High 19 none 1 Total Hazard Score High Moderate 9-11 Low 6-8 Minimal 0-5 None

137 Maximum Sele concentratio Hazard Scale Lemly Aquatic hazard Maximum Selenium concentration Units BEFORE PROJECT Sept Water µg/l 37.8 high 5 3 Sediment µg/g 0.8 none TABLE 3b. AQUATIC HAZARD ASSESSMENT OF SELENIUM IN SALT SLOUGH (LEMLY INDEX). Invertebrates µg/g 4.7 moderate Fish eggs µg/g 28.1 high Maximum Selen concentratio Bird eggs Hazard µg/g Scale 5.2 low Hazard 3 Scale 3.6 Lemly Aquatic hazard Maximum Selenium concentration Lemly Aquatic hazard Maximum Selenium concentration Hazard Scale Lemly Aquatic hazard Maximum Selenium concentration Units Units Maximum Selenium Lemly Aquatic Hazard Scale Maximum Selenium Lemly BEFORE Aquatic PROJECT Hazard Scale Maximum Selenium Lemly TOTAL Aquatic HAZARD SCORE Hazard Scale Maximum Selenium GRASSLAND Lemly Aquatic BYPASS PROJECT High Hazard Phase Scale I 18 concentration hazard concentration hazard concentration hazard concentration hazard Sept WY1997 WY1998 BEFORE PROJECT Water µg/l 37.8 high 5 GRASSLAND BYPASS PROJECT Phase I 3 moderate high GRASSLAND 5 BYPASS PROJECT 1.5 Phase Sept WY1997 WY1998 WY1999 Sediment µg/g 0.8 none none WY2000 low Water µg/l 37.8 high 5 3 moderate high minimal 2 Invertebrates µg/g 4.7 moderate Water minimal µg/l minimal low Sediment µg/g 0.8 none none low none 1 Fish eggs µg/g 28.1 high Sediment moderate µg/g moderate none Invertebrates µg/g 4.7 moderate minimal low minimal 2 Bird eggs µg/g 5.2 low Invertebrates minimal µg/g minimal Fish eggs µg/g 28.1 high moderate moderate moderate 4 TOTAL HAZARD SCORE Fish eggs µg/g 14.5 moderate High 18 Moderate 13 High 17 Bird eggs µg/g 5.2 low minimal minimal none 1 Bird eggs µg/g 4.9 minimal TOTAL HAZARD SCORE High 18 Moderate 13 High 17 Low 10 GRASSLAND BYPASS PROJECT Phase I TOTAL HAZARD SCORE Low GRASSLAND 11 BYPASS PROJECT Phase WY2000 WY2001 October 1, December 31, 2002 GRASSLAND BYPASS PROJECT Phase I GRASSLAND BYPASS PROJECT Phase II Water µg/l 1.7 minimal low minimal WY2000 WY2001 October 1, December 31, 2002 Calendar Year 2003 Sediment µg/g 0.7 none none Calendar Year none Water µg/l 1.7 minimal low minimal minimal 2 Invertebrates µg/g 2.7 minimal Water minimal µg/l minimal Sediment µg/g 0.7 none none none none 1 Fish eggs µg/g 14.5 moderate Sediment moderate µg/g moderate none Invertebrates µg/g 2.7 minimal minimal minimal minimal 2 Bird eggs µg/g 4.9 minimal Invertebrates minimal µg/g none Low Fish eggs µg/g 14.5 moderate moderate moderate moderate 4 TOTAL HAZARD SCORE Low 11 Fish eggs Moderate 12 µg/g 10.6 moderate Low Bird eggs µg/g 4.9 minimal minimal none none 1 Bird eggs µg/g 5.0 minimal TOTAL HAZARD SCORE Low 11 Moderate 12 Low 10 Low 10 TOTAL HAZARD SCORE GRASSLAND BYPASS PROJECT Phase II Moderate 12 Calendar Year 2004 Calendar Year 2005 Calendar Year 2006 GRASSLAND BYPASS PROJECT Phase II Water µg/l 1.1 minimal minimal minimal Grassland 2 Bypass Project Phase 1.0 II Calendar Year 2004 Calendar Year 2005 Calendar Year 2006 Calendar Year 2007 Sediment µg/g 0.6 none minimal Calendar Year none Water µg/l 1.1 minimal minimal minimal minimal 2 Invertebrates µg/g 3.3 Low Water moderate µg/l minimal Sediment µg/g 0.6 none Fish eggs 1 µg/g minimal 2 moderate none Sediment 1 moderate µg/g none 1 moderate none Invertebrates µg/g 3.3 Low Bird eggs 3 µg/g moderate minimal minimal Invertebrates low 2 µg/g high minimal none Fish eggs µg/g 10.6 moderate moderate moderate moderate 4 TOTAL HAZARD SCORE Fish eggs µg/g 13.4 moderate Moderate 12 Moderate 15 Low Bird eggs µg/g 5.0 minimal low none Bird eggs 1 µg/g none minimal TOTAL HAZARD SCORE Moderate 12 Moderate 15 Low 10 Moderate 13 Grassland Bypass Project Phase II TOTAL HAZARD SCORE Low Grassland 11 Bypass Project Phase III Calendar Year 2008 Calendar Year 2009 Calendar Year 2010 Grassland Bypass Project Phase II Grassland Bypass Project Phase III Water µg/l 1.0 minimal minimal minimal Grass Calendar Year 2008 Calendar Year 2009 Calendar Year 2010 Calendar Year 2011 Sediment µg/g 0.7 none none Calendar Year none <0.14 Water µg/l 1.0 minimal minimal minimal minimal 2 Invertebrates µg/g 2.1 minimal Water minimal µg/l minimal none Sediment µg/g 0.7 none none none 1 <0.14 none 1 Fish eggs µg/g 13.4 moderate Sediment low µg/g moderate none 4 1 < Invertebrates µg/g 2.1 minimal minimal minimal minimal 2 Bird eggs µg/g 3.1 minimal Invertebrates minimal µg/g none low Fish eggs µg/g 13.4 moderate low 3 20 moderate moderate 4 TOTAL HAZARD SCORE Low 11 Fish eggs Low 10 µg/g 12.8 moderate Low Bird eggs µg/g 3.1 minimal minimal none none 1 Bird eggs µg/g 3.6 minimal TOTAL HAZARD SCORE Low 11 Low 10 Low 10 Low 10 Grassland TOTAL Bypass HAZARD Project SCORE Phase III Low 11 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 135 Calendar Year 2012 Calendar Year 2013 Calendar Year 2014 Water µg/l Grassland Bypass Project Phase III 0.9 none none Hazard Scale minimal 2 Calendar Year 2012 Sediment µg/g Calendar Year none 1 Calendar Year 2014 <0.14 none Hazard Scale: 1 < none high 1 Water µg/l 0.9 none Invertebrates 1 µg/g none low minimal low moderate minimal 2 Sediment µg/g 0.3 none 1 <0.14 none 1 <0.78 none 1 Fish eggs µg/g 12.8 moderate low moderate low 4 Invertebrates µg/g 3.3 low low minimal 2 Bird eggs µg/g 3.6 minimal none minimal 2 Fish eggs µg/g 12.8 moderate low moderate 4 TOTAL HAZARD SCORE Low 11 Low none Low 11 Bird eggs µg/g 3.6 minimal none minimal 2 TOTAL HAZARD SCORE Low 11 Low 9 Low 11 Notes: Table prepared by US Fish and Total Wildlife Hazard Service, Score Sacramento. Hazard Scale: 5.0 high TOTAL HAZARD SCORE High 4.0 moderate Moderate 3.0 low 9-11 Low 2.0 minimal 6-8 Minimal 1.0 none 0-5 None Notes: Table prepared by US Fish and Wildlife Service, Sacramento. Notes: Table prepared by US Fish and Wildlife Service, Sacramento.

138 136 GRASSLAND BYPASS PROJECT TABLE 4a. MAXIMUM SELENIUM CONCENTRATION DATA USED FOR THE LEMLY INDEX (TABLE 4) FOR CALENDAR YEAR 2012 Mud Slough (north) below San Luis Drain MEDIA SAMPLE DATE LOCATION VALUE UNITS SAMPLE TYPE Water 19-Jun-12 Site I2, backwater below SLD discharge SAMPLE SIZE DATA SOURCE 23.0 μg/l weekly grab 1 USBR Sediment 28-Mar-12 Site I2, backwater below SLD discharge 1.0 μg/g (dry) whole core 1 USBR Invertebrates 22-Aug-12 Site D, Mud Slough below SLD discharge 6.3 μg/g (dry) Siberian freshwater shrimp 8 USFWS Fish eggs (*) 22-Aug-12 Site I2, backwater below SLD discharge 44.2 μg/g (dry) common carp 1 USFWS Bird eggs 8-May-12 Kesterson Unit along San Luis Drain 8.1 μg/g (dry) killdeer 1 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3 Salt Slough MEDIA SAMPLE DATE LOCATION VALUE SAMPLE TYPE Water Sediment Invertebrates Fish eggs (*) 24-Apr Sep Aug Mar-12 Site F, Salt Slough at Lander Ave Site F, Salt Slough at Lander Ave Site F, Salt Slough boat ramp, San Luis Unit Site F, Salt Slough boat ramp, San Luis Unit SAMPLE SIZE DATA SOURCE 0.9 μg/l weekly grab 1 USBR 0.3 μg/g (dry) whole core 1 USBR 3.3 μg/g (dry) Siberian freshwater shrimp 3 USFWS 12.8 μg/g (dry) redear sunfish 2 USFWS Bird eggs 22-Jun-12 San Luis Unit 3.6 μg/g (dry) killdeer 1 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3

139 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 137 TABLE 4b. MAXIMUM SELENIUM CONCENTRATION DATA USED FOR THE LEMLY INDEX (TABLE 4) FOR CALENDAR YEAR 2013 Mud Slough (north) below San Luis Drain MEDIA SAMPLE DATE LOCATION VALUE UNITS SAMPLE TYPE SAMPLE SIZE DATA SOURCE Water 11-Apr-13 Site D, Mud Slough below SLD discharge 14.0 μg/l weekly grab 1 USBR Sediment 29-Mar-13 Site I2, backwater below SLD discharge 0.4 μg/g (dry) whole core 1 USBR Invertebrates 21-Aug-13 Site D, Mud Slough below SLD discharge 18.8 μg/g (dry) backswimmer >20 USFWS Fish eggs (*) 21-Aug-13 Site D, Mud Slough below SLD discharge 71.9 μg/g (dry) Mississippi silverside 73 USFWS Bird eggs 30-Apr-13 Kesterson Unit along San Luis Drain 6.0 μg/g (dry) cliff swallow 3 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3 Salt Slough MEDIA SAMPLE DATE LOCATION VALUE SAMPLE TYPE SAMPLE SIZE DATA SOURCE Water 10-Jun-13 Site F, Salt Slough at Lander Ave 0.9 μg/l weekly grab 1 USBR Sediment 26-Sep-13 Site F, Salt Slough at Lander Ave <0.14 μg/g (dry) whole core 1 USBR Invertebrates 26-Mar-13 Site F, Salt Slough boat ramp, San Luis Unit 3.7 μg/g (dry) asian clam 2 USFWS Fish eggs (*) 26-Mar-13 Site F, Salt Slough boat ramp, San Luis Unit 13.9 μg/g (dry) bluegill 4 USFWS Bird eggs 30-Apr-13 San Luis Unit 2.7 μg/g (dry) killdeer 1 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3

140 138 GRASSLAND BYPASS PROJECT TABLE 4c. MAXIMUM SELENIUM CONCENTRATION DATA USED FOR THE LEMLY INDEX (TABLE 4) FOR CALENDAR YEAR 2014 Mud Slough (north) below San Luis Drain MEDIA SAMPLE DATE LOCATION VALUE UNITS SAMPLE TYPE SAMPLE SIZE DATA SOURCE Water 26-Jun-14 Site D, Mud Slough below SLD discharge 34.9 μg/l weekly grab 1 USBR Sediment 23-Sep-14 Site I2, backwater below SLD discharge 0.9 μg/g (dry) whole core 1 USBR Invertebrates 25-Jun-14 Site D, Mud Slough below SLD discharge 18.8 μg/g (dry) waterboatman >500 USFWS Fish eggs (*) 27-Aug-14 Site D, Mud Slough below SLD discharge μg/g (dry) Mississippi silverside 44 USFWS Bird eggs 13-Mar-14 Kesterson Unit along San Luis Drain 4.8 μg/g (dry) killdeer 1 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3 Salt Slough MEDIA SAMPLE DATE LOCATION VALUE SAMPLE TYPE SAMPLE SIZE DATA SOURCE Water 16-Dec-14 Site F, Salt Slough at Lander Ave 1.2 μg/l weekly grab 1 USBR Sediment 23-Sep-2014 / 24-Nov-2014 Site F, Salt Slough at Lander Ave <0.78 μg/g (dry) whole core 1 USBR Invertebrates 14-Mar-14 Site F, Salt Slough boat ramp, San Luis Unit 2.7 μg/g (dry) Siberian freshwater shrimp 27 USFWS Fish eggs (*) 14-Mar-14 Site F, Salt Slough boat ramp, San Luis Unit 9.8 μg/g (dry) red shiner 100 USFWS Bird eggs 26-Jun-14 San Luis Unit 3.0 μg/g (dry) killdeer 1 USFWS (*) fish egg selenium = fish wholebody selenium x 3.3

141 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 139 FIGURE 1a. MAP OF THE GRASSLAND BYPASS PROJECT

142 140 GRASSLAND BYPASS PROJECT FIGURE 1b. NUMBERS OF SIBERIAN FRESHWATER SHRIMP COLLECTED AT SITES IN SALT SLOUGH (SITE F) AND MUD SLOUGH UPSTREAM (SITE C), JUST DOWNSTREAM (SITE D) AND FARTHER DOWNSTREAM (SITE I/I2) OF THE SAN LUIS DRAIN OUTFALL. FIGURE 1c. RELATIONSHIP BETWEEN SURVIVAL OF BLUEGILL (LOGIT-TRANSFORMED) AND CONCENTRATION OF SELENIUM IN THEIR TISSUES AFTER 90 DAYS EXPOSURE TO DIETARY SELENIUM IN THE FORM OF SELENO-L-METHIONINE CLEVELAND ET AL. 1993).

143 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 141 FIGURE 1d. RELATIONSHIP BETWEEN SURVIVAL OF JUVENILE SALMON AND CONCENTRATION OF SELENIUM IN THEIR TISSUES AFTER 90 DAYS (CHINOOK SALMON: HAMILTON ET AL. 1990) OR 45 DAYS (ATLANTIC SALMON: POSTON ET AL. 1976) EXPOSURE TO DIETARY SELENIUM. THE 10% LETHALITY LEVEL (LC10=1.84 ΜG/G) DERIVED BY APPLYING THE BIPHASIC MODEL OF BRAIN AND COUSENS (1989) TO ONLY THE CHINOOK SALMON DATA IS CLOSE TO THE LC10 (1.85 ΜG/G) DETERMINED BY APPLYING THE BIPHASIC MODEL OF BECKON ET AL. (2008) TO ALL THE SALMON DATA SHOWN. THE CHINOOK SALMON DATA COMPRISES TWO SERIES OF DIETARY TREATMENTS, COMBINED HERE BECAUSE THE EFFECTS ON SURVIVAL ARE INDISTINGUISHABLE.

144 142 GRASSLAND BYPASS PROJECT FIGURE 1e. RELATIONSHIP BETWEEN GROWTH OF JUVENILE RAINBOW TROUT AND CONCENTRATION OF SELENIUM IN THEIR TISSUES AFTER 140 DAYS EXPOSURE TO DIETARY SELENIUM IN THE FORM OF SODIUM SELENITE (HILTON ET AL. 1980).

145 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 143 FIGURE 2. SELENIUM IN ALL FISH AND WATER COLLECTED IN SALT SLOUGH (SITE F). EACH DOT REPRESENTS A COMPOSITE SAMPLE. Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body (dry wt) and in water ( g/l) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Toxicity Concern Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 fish water Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 2a. SELENIUM IN MISSISSIPPI SILVERSIDES IN SALT SLOUGH (SITE F). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body (dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Toxicity Concern Mississippi silversides Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14

146 144 GRASSLAND BYPASS PROJECT FIGURE 2b. SELENIUM IN MISSISSIPPI SILVERSIDES IN SALT SLOUGH (SITE F). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body (dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Toxicity Concern Mississippi silversides Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 2c. SELENIUM IN MINNOWS IN SALT SLOUGH (SITE F). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Toxicity Concern minnow family Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 red shiner common carp goldfish Sacramento blackfish fathead minnow Sacramento splittail Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14

147 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 145 FIGURE 2d. SELENIUM IN SUNFISH AND BASS IN SALT SLOUGH (SITE F) Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Toxicity Concern Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 sunfish family Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 green sunfish bluegill sunfish,sp crappie, black/white largemouth bass Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 2e. SELENIUM IN VARIOUS FISH IN SALT SLOUGH (SITE F) Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern threadfin shad white catfish black bullhead channel catfish catfish sp striped bass logperch

148 146 GRASSLAND BYPASS PROJECT FIGURE 2f SELENIUM IN INVERTEBRATES AND WATER IN SALT SLOUGH (SITE F) Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Toxicity Concern Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 waterboatman backswimmer dragonfly/damselfly red crayfish Siberian freshwater shrimp isopod snail clam water Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 3. SELENIUM IN ALL FISH AND WATER SAMPLES IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Jan-92 Jan-93 Toxicity Concern Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 fish water Jan-12 Jan-13 Jan-14

149 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 147 FIGURE 3a. SELENIUM IN MOSQUITOFISH IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Jan-92 Jan-93 Toxicity Concern Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 mosquitofish Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 female male juvenile/mixed water Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 3b. SELENIUM IN MISSISSIPPI SILVERSIDES IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project 100 Selenium concentration (mg/kg dry wt) 10 1 Toxicity 0.1 Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Concern Mississippi silversides

150 148 GRASSLAND BYPASS PROJECT FIGURE 3c. SELENIUM IN MINNOWS IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Toxicity Concern Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 minnow family Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 red shiner common carp goldfish sacramento blackfish fathead minnow splittail Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 3d. SELENIUM IN SUNFISH AND BASS IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern sunfish family green sunfish bluegill sunfish,sp crappie, black/white largemouth bass

151 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 149 FIGURE 3e. SELENIUM IN VARIOUS FISH IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern threadfin shad white catfish black bullhead channel catfish catfish sp logperch sculpin Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 3f. SELENIUM IN INVERTEBRATES IN MUD SLOUGH ABOVE THE SAN LUIS DRAIN DISCHARGE (SITE C). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern waterboatman backswimmer giant water bug water beetle dragonfly/damselfly larva red swamp crayfish Siberian freshwater shrimp snail clam

152 150 GRASSLAND BYPASS PROJECT FIGURE 4. SELENIUM IN ALL FISH AND WATER SAMPLES IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Jan-92 Jan-93 Toxicity Concern Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 fish water Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 4a. SELENIUM IN MOSQUITOFISH IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern mosquitofish female male juvenile/mixed

153 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 151 FIGURE 4b. SELENIUM IN MISSISSIPPI SILVERSIDES IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern Mississippi silversides Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 4C. SELENIUM IN MINNOWS IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern minnow family red shiner common carp goldfish Sacramento blackfish fathead minnow Sacramento splittail

154 152 GRASSLAND BYPASS PROJECT FIGURE 4d. SELENIUM IN SUNFISH AND BASS IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern sunfish family green sunfish bluegill sunfish,sp crappie, black/white largemouth bass Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 4e. SELENIUM IN VARIOUS FISH IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Toxicity Concern threadfin shad white catfish black bullhead channel catfish catfish sp striped bass logperch sculpin

155 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 153 FIGURE 4f SELENIUM IN INVERTEBRATES AND WATER IN MUD SLOUGH BELOW THE SAN LUIS DRAIN DISCHARGE (SITE D). Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Jan-92 Jan-93 Jan-94 Jan-95 Toxicity Concern Jan-96 Jan-97 Jan-98 Jan-99 waterboatman backswimmer giant water bug water beetle dragonfly/damselfly larva red swamp crayfish Siberian freshwater shrimp Chinese mitten crab amphipod snail water Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 5. SELENIUM IN ALL FISH SAMPLES IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2) AND IN WATER AT SITE D, JUST BELOW THE DRAIN DISCHARGE. Site I Grassland Bypass Project Site I2 Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Jan-92 Jan-93 Toxicity Concern Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 fish water Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14

156 154 GRASSLAND BYPASS PROJECT FIGURE 5a. SELENIUM IN MOSQUITOFISH IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Site I Grassland Bypass Project Site I2 Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern mosquitofish female male juvenile/mixed Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 5b. SELENIUM IN MISSISSIPPI SILVERSIDES IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Grassland Bypass Project Site I Site I Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern Mississippi silversides

157 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 155 FIGURE 5c. SELENIUM IN MINNOWS IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Site I Grassland Bypass Project Site I2 Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern minnow family red shiner common carp goldfish Sacramento blackfish fathead minnow Sacramento splittail Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 5d. SELENIUM IN SUNFISH AND BASS IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Grassland Bypass Project Site I Site I Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern sunfish family green sunfish bluegill sunfish sp black crappie largemouth bass

158 156 GRASSLAND BYPASS PROJECT FIGURE 5e. SELENIUM IN VARIOUS FISH IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Site I Grassland Bypass Project Site I2 Selenium concentration in tissue ( g/g whole body dry wt) Toxicity Concern threadfin shad black bullhead channel catfish catfish sp sculpin striped bass Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 5f. SELENIUM IN INVERTEBRATES IN A MUD SLOUGH BACKWATER BELOW THE DRAIN DISCHARGE (SITES I AND I2). Grassland Bypass Project Site I Site I Jan-92 Jan-93 Jan-94 Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 Selenium concentration in tissue ( g/g whole body dry wt) and in water ( g/l) Toxicity Concern waterboatman backswimmer giant water bug water beetle dragonfly/damselfly larva red swamp crayfish Siberian freshwater shrimp other aquatic insects amphipod zooplankton snail water

159 CHAPTER 7a: BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES C, D, AND I2 157 FIGURE 6. SELENIUM IN FROG TADPOLES AT ALL SITES. Grassland Bypass Project 100 Selenium concentration in tissue ( g/g whole body dry wt) Jan-92 Jan-93 Jan-94 Toxicity Concern Mud Slough upstream (C) Mud Slough downstream (D) Mud Slough backwater (I) East Big Lake, near Mud Slough Salt Slough (F) Jan-95 Jan-96 Jan-97 Jan-98 Jan-99 Jan-00 Jan-01 Jan-02 Jan-03 Jan-04 Jan-05 Jan-06 Jan-07 Jan-08 Jan-09 Jan-10 Jan-11 Jan-12 Jan-13 Jan-14 FIGURE 7. SELENIUM IN ALL BIRD EGGS AT ALL SITES. 100 Grassland Bypass Project Selenium concentration ( g/g dry wt) 10 1 Toxicity Concern Mud Slough area Salt Slough area Merced Refuge San Joaquin River Refuge

160 158 GRASSLAND BYPASS PROJECT

161 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 159 7b BIOLOGICAL EFFECTS OF THE GRASSLAND BYPASS PROJECT AT SITES E, G, H AND R Andrew G. Gordus Ph.D. 1 Rachel McNeal 2 1 Staff Toxicologist, California Department of Fish and Wildlife East Shaw Avenue, Fresno, California (559) andy.gordus@wildlife.ca.gov 2 Environmental Scientist, California Department of Fish and Wildlife East Shaw Avenue, Fresno, California (559) rachel.mcneal@wildlife.ca.gov ABSTRACT In its sixteenth, seventeenth and eighteenth years of operation ( ), the Grassland Bypass Project continued to reduce the risk of selenium toxicity in the ecosystem from which the Project removed agricultural subsurface drainwater. However, it also continued to cause elevated risk in the waterway into which the drainwater has been diverted by the Project. In Mud Slough (north) (Site E) downstream from the outfall of the San Luis Drain (SLD), mean selenium concentrations in bait fish and invertebrates continued to exceed thresholds of concern. All bait fish samples exceeded 4 µg Se/g (dry weight) threshold of concern in whole-body fish and seven of thirteen samples exceeded the toxicity level (9 µg/g dry weight). Selenium concentrations did not exceed the 2 µg/g (wet weight) fish consumption guideline in five composite samples of carp (Cyprinus carpio) muscle tissue collected in 2012 in Mud Slough (north). No carp was caught in 2013 and 2014 because of extreme low flows as a result of the drought. In 2012 and 2013, both Siberian freshwater shrimp (Exopalaemon modestus) samples exceeded 3 µg Se/g (dry weight) waterbird dietary threshold and above the 7 µg/g (dry weight) dietary toxicity threshold. In the San Joaquin River at Fremont Ford (Site G), upstream of Mud Slough (north), mean selenium concentrations in bait fish and invertebrates remained below thresholds of concern. All carp muscle tissue samples collected at this site in 2012 and 2013 remained below the 2 µg Se/g (wet weight) fish consumption guideline. No carp was caught at this site in All Siberian freshwater shrimp samples were below the 3 µg Se/g (dry weight) level of concern. In the San Joaquin River at Hills Ferry (Site H), downstream of the Mud Slough (north), two of four mean selenium concentrations in whole-body bait fish exceeded the 4 µg/g (dry weight) threshold of concern in samples collected in One sample of Siberian freshwater shrimp was slightly above the 3 ug Se/g level of concern. All eight samples of carp muscle tissue collected at this site were below the 2 µg Se/g fish consumption guideline. No carp was collected at Site H in Last monitoring at this site was May The U.S. Bureau of Reclamation (Reclamation) moved the location for collecting biological samples in the San Joaquin River from Hills Ferry upstream to a point within the CDFW Grasslands Wildlife Area China Island Unit (Site R). The reason for this change is to obtain samples from that portion of the river that is most likely affected by the conveyance of agricultural drain water from the Grasslands Drainage Area (GDA). Monitoring at Site R started in July In the San Joaquin River at China Island, upstream from Hills Ferry, some selenium concentrations in whole-body bait fish exceeded the 4 µg/g (dry weight) threshold of concern but below the toxicity level (9 µg/g dry weight) in all samples collected in 2013 and All selenium concentrations of Siberian freshwater shrimp were slightly above the 3 ug/g level of concern. There were no carp muscle tissue collected at this site in 2013 and 2014 due to very low flows. In 2012, 2013 and 2014, selenium in all seed samples collected along Mud Slough (Site E) remained below the 3 µg/g (dry weight) dietary level of concern for waterbirds. Boron concentrations in all seed samples along Mud Slough were above the 30 µg/g (dry weight) threshold of concern as diet for waterbirds. Along the San Joaquin River above the Mud Slough confluence (near Fremont Ford) (Site G), the concentrations of selenium in bulrush seed remained well below the 3 µg/g (dry weight) dietary level of concern for waterbirds.

162 160 GRASSLAND BYPASS PROJECT However, in 2013, boron concentrations in bulrush seed in two of three samples were above the 30 µg/g (dry weight) threshold of concern as diet for waterbirds. No samples exceeded the threshold of concern in 2012 and Along the San Joaquin River below the Mud Slough confluence (Hills Ferry) (Site H) and at the San Joaquin River at China Island (Site R), the concentrations of selenium in bulrush seed heads remained below the 3 ug/g level of concern. Boron concentrations of in all samples of bulrush seeds collected in 2012 were above the 30 µg Se/g (dry weight) threshold of concern as diet for waterbirds. METHODS Agency Responsibilities The California Department of Fish and Wildlife (CDFW) agreed to conduct the biomonitoring portion of the Compliance Monitoring Program for three sites. The methods used by the CDFW are described in the Quality Assurance Project Plan (QAPP) for Use and Operation of the Grassland Bypass Project (USBR, 2001). These methods are also based on standard operating procedures described in Standard Operation Procedures for Environmental Contaminant Operations (USFWS, 1995) and standards used by the other agencies participating in the compliance monitoring program. Matrices Sampled Samples of the biota were collected at each site and analyzed for selenium and boron. Aquatic specimens were collected with dip nets, seine nets, funnel nets and by electro fishing. Mosquitofish (Gambusia affinis), inland silversides (Menidia beryllina), red shiners (Cyprinella lutrensis), carp (Cyprinus carpio), white catfish (Ameiurus catus), bluegill (Lepomis macrochirus), fathead minnow (Pimephales promelas) and bigscale logperch (Percina macrolepida) were the principal species of fish collected. Waterboatmen (family: Corixidae), backswimmers (family: Notonectidae), and red swamp crayfish (Procambarus clarkii) and Siberian freshwater shrimp (Exopalaemon modestus) were the principal invertebrates collected. Separation of biological samples from unwanted material also collected in the nets was accomplished by using Teflon sieves. To the extent possible, three replicate, composite samples (minimum 5 individuals totaling at least 2 grams (preferably 5 grams) for each composite) of each primary species listed above were collected. Bait fish were analyzed as composite whole-body samples and muscle tissue from carp were analyzed. Analyses of fish samples collected from the San Joaquin River (Sites G, H and R) and Mud Slough (Site E) were prioritized to first meet the objectives of the Compliance Monitoring Plan (Section ). The seed heads of wetland plants that provide food for waterfowl were collected in the late summer (August) of each year. This plant material was analyzed for boron as well as selenium. Plankton and aquatic insect composite samples were collected from Site E, G, H and R using two plankton nets of similar diameter and mesh size. The nets were left in the river at a specific length of time depending on the flow (measured using Global Water Flow Probe Model FP111). Monitoring started in May The objective was to consistently sample acre foot (30,000 gallons) of equivalent water flow at each location and sampling period. All biota samples were kept on ice or on dry ice while in the field then kept frozen to zero degrees centigrade (0 C) during storage and shipment. For all samples, after freeze drying, homogenization, and nitric digestion, total selenium was determined by hydride generation atomic absorption spectrophotometry and boron was determined by inductively coupled (argon) plasma spectroscopy. Sampling Sites Site E is located where Mud Slough crosses State Highway 140 and is located upstream from the confluence with the San Joaquin River. This site represents the lower reach of the slough that is contaminated by the operation of the Project. This point along Mud Slough is within the flood plain of the San Joaquin River, so flows are slower. Flood waters of the San Joaquin River periodically back up into slough, providing some flushing. Site G is located on the San Joaquin River and State Highway 140 at Freemont Ford, upstream of the Mud Slough confluence. This site represents the reach of the San Joaquin River that is no longer contaminated with agricultural

163 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 161 drainwater from the Grassland Drainage Area as a result of the GBP. Site H is located at Hills Ferry on the San Joaquin River about two river miles downstream of the Mud Slough confluence. This site represents the reach of the San Joaquin River most strongly influenced by agricultural drain water discharged by the GBP. One of the environmental commitments of the GBP is that it will not worsen water quality in the San Joaquin River. For practical reasons of year-round accessibility, the site was located just upstream of the Merced River confluence; Merced River waters have relatively low concentrations of selenium. Monitoring ceased at Site H and no samples have been collected after May It was suggested Merced River flows influence the selenium results at Site H. To determine if Merced River had any influence, the sampling site was moved 1.5 river miles upstream from Site H to within the China Island Wildlife Area (Site R). Sampling started July 2013 and had been suggested to show the full influence of the Grassland Bypass Project on the river. Sampling Times Since 1995, CDFW biota sampling has been synchronized to occur during the months of November (December), March, June, and August (September). Departures from the Monitoring Plan and Quality Assurance Project Plan All biological samples beginning in 1999 have been analyzed at the Water Pollution Control Laboratory of the CDFW in Rancho Cordova, California, after this laboratory was screened and approved by the GBP Quality Control Officer. RESULTS Mud Slough at Highway 140 (Site E) Selenium in Fish The concentration of selenium from the only sample of whole-body mosquitofish collected during 2012 was 5.23 µg/g (dry weight) ( Table 1). In 2013, five composite samples of whole-body mosquitofish collected ranged from 4.67 to 11.8 µg Se/g (dry weight). Eleven composite samples of whole-body mosquitofish collected during 2014 ranged from 8.57 to 20.9 µg Se/g (dry weight) ( Table 1). In 2013, mean concentrations were 4.67, 8.54 and 11.8 µg/g (dry weight) and in 2014 were 9.70, 8.69, 20.6 and 12.1 µg/g (dry weight) ( Table 1). There were three composite inland silverside samples collected in 2012 and six composite samples collected in Three composite samples ranged from 4.22 to 8.01 µg Se/g (dry weight) in 2012 and from 10.1 to 18.7 µg/g (dry weight) in 2013 ( Table 1). No inland silverside was collected at Site E in In 2013, there were three composite samples each of fathead minnow and red shiner collected at Site E. The selenium concentrations in fathead minnows ranged from 9.32 to 9.82 µg/g (dry weight) and the red shiners had selenium concentration ranged from 5.11 to 5.76 µg/g (dry weight) ( Table 1). There were no samples for both species collected in 2012 and Selenium in Invertebrates One composite red crayfish sample was collected at Site E in 2012 and had a selenium concentration of 4.72 µg/g (dry weight) and in 2014, two composite sample ranged from 3.92 µg/g (dry weight) to 9.74 µg/g (dry weight) ( Table 1). No red crayfish was collected in Three Siberian freshwater shrimp composite samples collected in 2012 ranged from 9.23 to 10.7 µg Se/g (dry weight) and one composite sample collected in 2013 had 10.4 µg Se/g (dry weight) ( Table 1). No shrimp samples were collected in In 2014, two composite snail samples had a mean concentration of 2.43 µg Se/g (dry weight) ( Table 1). Only one sample of aquatic insects was collected in 2012 (5.02 µg Se/g dry weight) and one in 2014 (15.4 µg Se/g dry weight). There were thirteen composite plankton invertebrate samples collected in 2013 and 2014 at Site E that ranged from to 9.03 µg Se/g (dry weight) ( Table 1).

164 162 GRASSLAND BYPASS PROJECT Selenium in Plants All nine composite samples of bulrush seed heads that were collected in Site E in 2012, 2013 and 2014 (see Table 1) ranged from to 2.8 µg Se/g (dry weight). Boron in Plants The mean boron concentration collected at this site in 2012 was 58.6 µg/g (dry weight); in 2013 was 75.8 µg/g (dry weight); and in 2014 was 137 µg/g (dry weight) ( Table 1). Site E Summary In summary, all eight mean selenium concentrations for mosquitofish ( Table 1) were above the level of concern for whole-body warm water fish (4 µg/g dry weight) and four were above the toxicity threshold of 9 µg/g (dry weight) ( Table 1). All five fathead minnow, red shiner and silverside means were above 4 ug Se/g and three were above 9 ug Se/g ( Table 1). All three red crayfish means were above 3 µg Se/g waterbird dietary level of concern and one was above 7 µg Se/g waterbird dietary toxicity threshold ( Table 1). Both Siberian freshwater shrimp were above the 7 µg Se/g threshold. Five of seven composite sample means were below the 3 µg Se/g threshold and two samples were above 3 µg Se/g, but were below the 7 ug Se/g threshold ( Table 1). Both aquatic insect samples were above 3 µg/g with one sample above the 7 ug/g threshold ( Table 1). All three plant samples were below 3 µg Se/g threshold. All three plant samples were above the 30 µg/g threshold for boron ( Table 1). Total discharge into the San Luis Drain at Site A has decreased from 52,820 acre-feet (ac-ft)(years ) and 41,870 ac-ft (years ) to 22,680 ac-ft for years 2012 to The same is true for discharge in to Mud Slough at Site B decreasing from 59,740 ac-ft and 45,650 ac-ft to 28,550 ac-ft across the same years. Flows during 2014 were non-existence during the year as a result of source control reduction activities by the Grassland Basin Drainers and the long term drought. There was an increase in aquatic biota selenium concentrations from 2012 to 2014 which is most likely from evapotranspiration and shallow groundwater seepage, which is eight to twelve feet below the ground surface, which has elevated salts and trace elements. San Joaquin River at Fremont Ford (Site G) Selenium in Fish Selenium concentrations in samples of fish collected from this site during 2012, 2013 and 2014 continued to reflect removal of selenium-laden drainwater. Twenty-four composite samples of whole-body mosquitofish collected during 2012, 2013 and 2014 ranged from 1.24 to 1.72 µg/g (dry weight) ( Table 1). Three composite bigscale logperch samples were collected in 2012 with a range from 2.04 to 2.14 µg Se/g (dry weight) ( Table 1). In 2013, four composite inland silverside samples were collected and one composite sample in Selenium concentrations ranged from 1.21 to 1.49 µg/g (dry weight) ( Table 1). There was no sample collected in Three red shiner composite samples were collected in 2013 and four in 2014 and ranged from 1.34 to 2.09 µg Se/g (dry weight) ( Table 1). Selenium in Invertebrates Selenium concentrations in all invertebrates collected from this site during 2012, 2013 and 2014 continue to be well below the threshold of concern for invertebrates as prey items. Composite samples of red crayfish, Siberian freshwater shrimp, snails, aquatic insects (waterboatmen, dragonfly nymph and giant water bug) and a tadpole were collected in Site G. There were seven composite red crayfish samples collected in Site G in 2012, 2013 and The selenium concentrations ranged from 0.71 to 1.50 µg/g (dry weight) ( Table 1). Eight composite Siberian freshwater shrimp samples were collected in 2012 and The selenium concentration ranged from 1.86 to 2.89 µg/g (dry weight) ( Table 1). There was no sample collected in Only two composite snail samples were collected in 2012 and the selenium mean concentration was µg/g (dry weight) ( Table 1). No sample was collected in 2013 and A tadpole composite sample was collected in 2013 and the selenium concentration was 1.60 µg/g (dry weight) ( Table 1). Two composite aquatic insect samples were collected in 2012 and The composite aquatic insect samples were waterboatmen, dragonfly nymph and giant water bug and ranged from and 1.05 µg Se/g (dry weight) ( Table 1). There were sixteen composite plankton samples collected in 2013 and 2014 and ranged from to 2.39 µg Se/g (dry weight) ( Table 1).

165 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 163 Selenium in Plants Nine composite bulrush seed heads were collected in 2012, 2013 and 2014 had selenium mean concentrations of 0.143, and 0.76 µg/g (dry weight), respectively and ranged from to 1.92 µg Se/g across years ( Table 1). Boron in Plants There were nine composite bulrush seedheads collected at Site G in 2012, 2013 and 2014 and the mean boron concentrations were 22.9, 42.7 and 26.4 µg/g (dry weight), respectively. In 2013, the mean concentration exceeded the 30 ug/g (dry weight) threshold of concern ( Table 1). The composite boron concentrations ranged from 27.4 to 57.1 µg/g (dry weight). Summary In summary, all mean selenium concentrations for mosquitofish, red shiners, silversides and bigscale logperch were below the level of concern for whole-body warm water fish (4 µg/g dry weight) and the toxicity threshold of 9 µg/g (dry weight) ( Table 1). Selenium concentrations in whole-body mosquitofish have consistently been below the 4 µg/g (dry weight) level of concern since the GBP began September All red crayfish, Siberian freshwater shrimp, tadpole, aquatic insects and plants were below the threshold of concern (3 µg/g dry weight) for birds that may forage on these invertebrates and the dietary toxicity threshold (7 µg/g dry weight) ( Table 1). One plant sample was above the 30 µg/g threshold for boron ( Table 1). San Joaquin River Below Mud Slough (Site H) Selenium in Fish The selenium concentration from the only mosquitofish sample caught in 2012 was 4.22 µg/g (dry weight) ( Table 1). In 2012 and 2013, six inland silverside composite samples ranged from 2.47 to 4.67 µg Se/g (dry weight) ( Table 1). In 2013, three red shiner composite samples ranged from 2.04 to 2.40 µg Se/g (dry weight) ( Table 1). Selenium in Invertebrates Selenium concentrations in two composite Siberian freshwater shrimp samples were 3.62 and 3.45 µse/g (dry weight) ( Table 1). No composite shrimp sample collected in Three plankton composite plankton samples collected at Site H in 2012 and 2013 ranged from 1.06 to 3.26 µg Se/g (dry weight) ( Table 1). Selenium in Plants In 2012, bulrush seed head composite samples ranged from to µg Se/g (dry weight) and the mean was µg Se/g (dry weight) ( Table 1). Boron in Plants Boron concentrations in all three composite samples collected in 2012 ranged from 31.2 to 36.1 µg/g (dry weight). Summary In summary, mean selenium concentrations in mosquitofish was a little above the level of concern for whole-body warm water fish (4 µg/g dry weight) and below the toxicity threshold of 9 µg/g (dry weight) ( Table 1). The red shiner was below 4 µg Se/g. One of two silverside was below 4 ug/g and both were below 9 ug/g ( Table 1). The only Siberian freshwater shrimp mean concentration was above the 3 µg/g threshold, but below the 7 ug/g threshold ( Table 1). All three plant samples were below 3 µg Se/g threshold ( Table 1) and all three plant samples were above the 30 µg/g threshold for boron ( Table 1).

166 164 GRASSLAND BYPASS PROJECT San Joaquin River at China Island Wildlife Area (Site R) Selenium in Fish Sixteen composite mosquitofish samples were collected in 2013 and 2014 and the selenium concentrations ranged from 3.15 to 6.98 µg/g (dry weight) ( Table 1). In 2013, four composite inland silverside samples ranged from 4.35 to 8.13 µg Se/g (dry weight) ( Table 1). No samples were collected in In 2014, four composite red shiner samples ranged from 3.24 to 4.25 µg Se/g (dry weight) ( Table 1). No red shiners were caught in Selenium in Invertebrates Four composite red crayfish samples were collected during 2014 ranged from 2.23 to 4.78 µg Se/g (dry weight) ( Table 1). No red crayfish sample was collected at Site R in Six composite Siberian freshwater shrimp samples were collected in 2013 where the selenium concentrations ranged from 3.42 to 4.68 µg/g (dry weight). The only composite sample collected in 2014 had 4.20 µg Se/g (dry weight) ( Table 1). In 2013 and 2014, the fourteen composite plankton samples had selenium concentrations ranging from to 2.85 µg/g (dry weight) ( Table 1). Selenium in Plants In 2013 and 2014, three composite samples of white sweet clover seed heads and three composite samples of bulrush seed heads were collected, respectively. The selenium concentrations ranged from to µg/g (dry weight) ( Table 1). Boron in Plants Boron concentrations in all composite samples of waterbird forage plant material (seed heads) collected in 2013 and 2014 ranged from 35.5 to 88.9 µg/g (dry weight) ( Table 1). Site R Summary In summary, one of six mean selenium concentrations for mosquitofish was below the level of concern for wholebody warm water fish (4 µg/g dry weight) but all were below the 9 µg/g toxicity threshold ( Table 1). One of four composite samples of red shiner and all four composite samples of inland silversides were above 4µg/g. All red shiner and silverside samples were below 9µg/g ( Table 1). Two red crayfish were above the threshold of concern (3 µg/g dry weight) for birds that may forage on these invertebrates and below the dietary toxicity threshold (7 µg/g dry weight) ( Table 1). All four Siberian freshwater shrimp were above the 3 µg/g threshold. Both plant samples means were below the 3 µg Se/g threshold and were above the 30 µg/g threshold for boron ( Table 1). Fish Community Assessment Fish community assessments are conducted to describe species richness, abundance and community structure. Fish populations were sampled in Mud Slough at Highway 140 (Site E), San Joaquin River at Fremont Ford (Site G), San Joaquin River below Mud Slough (Site H) and San Joaquin River at China Island Wildlife Area (Site R). Tables 2a-2e is a compilation of the 44 fish species (n = 49,146), that have been collected at these sites between March 2001 and December Twelve species of native fish have been caught. The native species were Sacramento blackfish (Orthodon macrolepidotus), splittail (Pogonichthys macrolepidotus), Sacramento sucker (Catostomus occidentalis), prickly sculpin (Cottus asper), Chinook salmon (Oncorhynchus tshawystcha), Sacramento pikeminnow (Ptychocheilus grandis), hitch (Lavinia exilicauda), California roach (Hesperoleucus symmetricus), Tule perch (Hysteocarpus traski), hardhead (Mylopharodon conocephalus) and the riffle sculpin (Cottus golosus). From 2012 to 2014, only three species of native fish had been caught. At Site E, two Sacramento splittail were caught in At Site G, four riffle sculpin and seven Sacramento sucker were caught in At Site H, there were three Sacramento sucker and four riffle sculpin caught in 2012.

167 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 165 There is a fish screen, which is set up in September through early December, at Site H to prevent fall-run salmon from moving upstream to the sampling sites for this project. Sacramento blackfish was the most abundant native fish at the three sites throughout the study. The most common non-native fish were mosquitofish, inland silversides, carp, and red shiner. Assessment of Risk to Public Health from Consumption of Fish A public health advisory on consumption of fish is in effect for the Grasslands area (OEHHA 2001): Because of elevated selenium levels, no one should eat more than four ounces of fish from the Grassland area, in any two-week period. Women who are pregnant or may become pregnant, nursing mothers, and children age 15 and under should not any eat fish from this area. To assess current human health risks due to selenium in gamefish, carp were collected from Mud Slough (Site E) and the San Joaquin River (Sites G, H and R). Samples of skinless fillets from these fish were analyzed for selenium and compared with the 2 µg/g wet weight interim internal guidance and screening level for selenium established by the Office of Environmental Health Hazard Assessment (OEHHA). Selenium concentrations from five composite carp muscle samples collected at Site E during 2012 ranged from to 1.46 µg/g (wet weight) ( Table 1). There were no carp collected at Site E in 2013 and 2014 due to low water flows. At Site G there were ten composite samples collected in 2012 and two samples in No carp were collected in The 2012 selenium concentrations ranged from to µg/g (wet weight) and in 2013 ranged from and µg/g (wet weight) ( Table 1). At Site H, there were eight composite carp muscle tissue collected in 2012 which ranged from to 1.19 µg Se /g (wet weight) ( Table 1). There were no carp collected at Sites H and R in 2013 and The concentrations of selenium in all carp muscle tissue collected at Site H remained well below the 2µg/g health screening level for human consumption( Table 1). Acknowledgments We greatly appreciate the assistance provided in the field by Abimael Leon Cardona and Erica Rhyne-Christensen from California Department of Water Resources; Stacy Brown and Gabe Poduska from the Bureau of Reclamation and Kelley Aubushon, Matt Bigelow, Kyle Brinsendine, Pat Ferguson, Kevin Gipson, Mike Grill, Thomas Gromis, Eric Guzman, Abigail Gwinn, Mike Hubble, Steve Hulbert, Ken Johnson, Amy Krisch, Ben Lewis, Brian Mahardja, Jamie McGrath-Castro, Sara Morrison, John Shelton, Todd Stansberry, Kyle Stoner, Erin Tennant, Dyana Valencourt, Jim Vang and Rachel Walker helped collect samples for CDFW. Tables Table 1. Biotic selenium and boron results for the Grassland Bypass Project at Mudslough and the San Joaquin River. Table 2a. Community Assessment of Fish Caught By CDFG Table 2b. Community Assessment of Fish Caught by CDFG Table 2c. Community Assessment of Fish Caught by CDFG Table 2d. Community Assessment of Fish Caught by CDFG Table 2e. Community Assessment of Fish Caught by CDFG

168 166 GRASSLAND BYPASS PROJECT TABLE 1. BIOTIC SELENIUM AND BORON RESULTS FOR THE GRASSLAND BYPASS PROJECT AT MUDSLOUGH AND THE SAN JOAQUIN RIVER. FISH (ΜG/G WET WT.) FISH (ΜG/G DRY WT.) INVERTEBRATES (ΜG/G DRY WT.) PLANTS (ΜG/G DRY WT.) SITE YEAR MONTH CARP BIGSCALE LOGPERCH MOSQUITOFISH FATHEAD MINNOW RED SHINERS INLAND SILVERSIDE BULLFROG/TADPOLE RED CRAYFISH SIBERIAN FRESWATER SHRIMP SNAILS COMPOSITE AQUATIC INSECTS Site E (Mudslough) 2012 (SE) (B) MAR Mean 1.03 JUN Mean AUG Mean DEC Mean MAY Mean JUL Mean OCT Mean DEC Mean MAR Mean JUN Mean AUG Mean DEC Mean

169 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 167 TABLE 1. BIOTIC SELENIUM AND BORON RESULTS FOR THE GRASSLAND BYPASS PROJECT AT MUDSLOUGH AND THE SAN JOAQUIN RIVER. (CONT.) FISH (ΜG/G WET WT.) FISH (ΜG/G DRY WT.) INVERTEBRATES (ΜG/G DRY WT.) PLANTS (ΜG/G DRY WT.) SITE YEAR MONTH CARP BIGSCALE LOGPERCH MOSQUITOFISH FATHEAD MINNOW RED SHINERS INLAND SILVERSIDE BULLFROG/TADPOLE RED CRAYFISH SIBERIAN FRESWATER SHRIMP SNAILS Site G Hwy 140) COMPOSITE AQUATIC INSECTS (SE) (B) 2012 MAR Mean JUN Mean AUGt Mean DEC Mean MAY Mean JUL Mean OCT Mean DEC Mean MAR Mean JUN Mean AUG Mean DEC Mean

170 168 GRASSLAND BYPASS PROJECT TABLE 1. BIOTIC SELENIUM AND BORON RESULTS FOR THE GRASSLAND BYPASS PROJECT AT MUDSLOUGH AND THE SAN JOAQUIN RIVER. (CONT.) FISH (ΜG/G WET WT.) FISH (ΜG/G DRY WT.) INVERTEBRATES (ΜG/G DRY WT.) PLANTS (ΜG/G DRY WT.) SITE YEAR MONTH CARP BIGSCALE LOGPERCH MOSQUITOFISH FATHEAD MINNOW RED SHINERS INLAND SILVERSIDE BULLFROG/TADPOLE RED CRAYFISH Site H Hills Ferry) 2012 SIBERIAN FRESWATER SHRIMP SNAILS COMPOSITE AQUATIC INSECTS (SE) (B) MAR Mean JUN Mean AUG Mean DEC Mean MAY Mean Site R China Island Wildlife Area) JUL Mean OCT Mean DEC Mean MAR Mean JUN Mean AUG Mean DEC Mean Backswimmers and Waterboatman 2 Dragonfly nymph 3 Dragonfly nymph and Giant waterbug 4 Bulrush 5 White sweet clover

171 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 169 TABLE 2a. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG MUD SLOUGH AT HIGHWAY 140 (SITE E) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLED Mosquitofish Gambusia affinis Introduced I T F IIE E USA pp ,952 Carp Cyprinus carpio Introduced O T F IIE Europe pp ,175 Red shiner Cyprinella lutrensis Introduced O T F IIE M USA pp Inland silverside Menidia beryllina Introduced I M F IIE SE USA pp Goldfish Carrrassius auratus Introduced O T F IID Japan pp Snail sp. Introduced O 193 Shrimp species Introduced O M E,F IIE 161 White catfish Ameiurus catus Introduced I/P T F IID E USA pp Red crayfish Procambarus (Scapulicambarus) Introduced O T F IIE 123 clarkii Fathead minnow Pimephales promelas Introduced O T F IIE M USA pp Largemouth bass Micropterus salmoides Introduced P T F IID M USA pp Bluegill Lepomis macrochirus Introduced I T F IID M USA pp Green sunfish Lepomis cyanellus Introduced I/P T F IID M USA pp Brown bullhead Ameiurus nebulosus Introduced I/P T F IID M USA pp Threadfin shad Dorosama petenese Introduced I M F IID SE USA pp Sacramento Orthodon blackfish microlepidotus Native O T F IE pp Spotted bass Micropterus punctulatus Introduced P M F IIE SE USA pp Channel catfish Ictalurus punctatus Introduced I/P M F IID M USA pp Prickly sculpin Cottus asper Native I M AM,E,F IE pp Redear sunfish Lepomis microlophus Introduced I M F IID SE USA pp Golden Shiner Notemigonus crysoleucas Introduced I M F IIE E USA pp Black bullhead Ameiurus melas Introduced I/P T F IID E USA pp Mylopharodon Hardhead Native O M F IC pp conocephalus Pomoxis Black crappie Introduced I/P M F IID M USA pp nigromaculatus Hesperoleucus California roach symmetricus Native I M F ID pp symmetricus Striped bass Morone saxatilis Introduced P M AN IID E USA pp White crappie Pomoxis annularis Introduced I/P T F IID M USA pp Sacramento Splittail Pogonichthys macrolepidotus Native O M E,F IB pp Hitch Lavinia exilicauda Native O M F ID pp Mirror carp Cyprinus carpio Introduced O T F IIE Europe pp Sacramento pikeminnow Ptychocheilus grandis Native I/P M F IE pp Sacramento Catostomus sucker occidentalis Native O M F IF pp Smallmouth bass Micropterus dolomieui Introduced I/P M F IID M USA pp American shad Alosa sapidissima Introduced I M AN IID E USA pp Bigscale logperch Percina macrolepida Introduced I T F IID SW USA pp Bullfrog Rana catesbeiana Introduced O T IIE - Chinook salmon Oncorhynchus tshawytscha Native I I AN, F IB pp Green x Redear Lepomis ssp. Introduced I M F IID -

172 170 GRASSLAND BYPASS PROJECT TABLE 2a. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG MUD SLOUGH AT HIGHWAY 140 (SITE E) (CONT.) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLED Green sunfish/ Bluegill Hybrid Pacific lamprey Lampetra tridentata Native O T AN, F ID pp Pacific staghorn sculpin Leptocottus armatus Native I M E,F IE pp Pumpkin seed Lepomis gibbosus Introduced I T F IID pp Riffle sculpin Cottus gulosus Native I M F ID pp River lamprey Lampetra ayresi Native O M AN, F ID pp Shimofuri goby Tridentiger bifasciatus Introduced O M E IIE Japan pp Speckled dace (Sacramento) Threespine stickleback Rhinichthys osculus carringtoni Gasterostreus aculeatus Native I T F IE pp Native O M AN, E, F IE pp Tule perch Hysteocarpus traski Native I I E,F ID pp Turtle, pond - Warmouth Lepomis gulosus Introduced I M F IIC M USA pp Yellowfin goby Acanthogobius flavimanus Introduced O M F IID E Asia pp Total Samples 15,777 - Data source: California Department of Fish and Game. Community Assessment of Fish Caught By CDFG 19 Mar Dec 2011 (34 trips) Abbreviations Trophic Level: Tolerance to Degradation: Status*: O: omnivorous (includes omnivores, herbivores, general planktivores) I: invertivore (includes invertivores, zooplanktivores I/P: carnivore (includes piscivores, large invertebrates (crayfish), amphibian, and mammalian predators I: intolerant Life Style*: AM: amphidromous M: moderately tolerant AN: anadromous T: Tolerant E: estuarine resident F: freshwater resident I. Native species A. Extinct/extirpated B. Threatened or endangered C. Special concern D. Watch list E. Stable of increasing *Adapted from Moyle, Peter, Inland Fishes of California. University of California Press. Berkeley, California.

173 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 171 TABLE 2b. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT FREMONT FORD (SITE G) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTALS Mosquitofish Gambusia affinis Introduced I T F IIE E USA pp ,704 Carp Cyprinus carpio Introduced O T F IIE Europe pp Red shiner Cyprinella lutrensis Introduced O T F IIE M USA pp Shrimp species Introduced O M E,F IIE 842 Bluegill Lepomis macrochirus Introduced I T F IID M USA pp White catfish Ameiurus catus Introduced I/P T F IID E USA pp Largemouth bass Micropterus salmoides Introduced P T F IID M USA pp Inland silverside Menidia beryllina Introduced I M F IIE SE USA pp Procambarus Red (Scapulicambarus) Introduced O T F IIE 268 crayfish clarkii Carrrassius Goldfish Introduced O T F IID Japan pp auratus Threadfin shad Dorosama petenese Introduced I M F IID SE USA pp Green sunfish Lepomis cyanellus Introduced I/P T F IID M USA pp Ictalurus Channel catfish Introduced I/P M F IID M USA pp punctatus Lepomis Redear sunfish Introduced I M F IID SE USA pp microlophus Micropterus Spotted bass Introduced P M F IIE SE USA pp punctulatus Fathead Pimephales Introduced O T F IIE M USA pp minnow promelas Snail sp. Introduced O 64 Bigscale logperch Percina macrolepida Introduced I T F IID SW USA pp Bullfrog Rana catesbeiana Introduced O T IIE 48 Striped bass Morone saxatilis Introduced P M AN IID E USA pp Black crappie Sacramento blackfish Sacramento sucker Pomoxis nigromaculatus Orthodon microlepidotus Catostomus occidentalis Introduced I/P M F IID M USA pp Native O T F IE pp Native O M F IF pp Hitch Lavinia exilicauda Native O M F ID pp Sacramento Splittail Brown bullhead Pogonichthys macrolepidotus Ameiurus nebulosus Native O M E,F IB pp Introduced I/P T F IID M USA pp Riffle sculpin Cottus gulosus Native I M F ID pp Black bullhead Ameiurus melas Introduced I/P T F IID E USA pp Warmouth Lepomis gulosus Introduced I M F IIC M USA pp California roach Prickly sculpin Chinook salmon Hesperoleucus symmetricus symmetricus Native I M F ID pp Cottus asper Native I M AM,E,F IE pp Oncorhynchus tshawytscha Native I I AN, F IB pp

174 172 GRASSLAND BYPASS PROJECT TABLE 2b. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT FREMONT FORD (SITE G). (CONT.,) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTALS Golden Shiner Green sunfish/ Bluegill Hybrid Notemigonus crysoleucas Introduced I M F IIE E USA pp Green x Redear Lepomis ssp. Introduced I M F IID 1 Pumpkin seed Sacramento pikeminnow Lepomis gibbosus Introduced I T F IID pp Ptychocheilus grandis Native I/P M F IE pp White crappie Pomoxis annularis Introduced I/P T F IID M USA pp American shad Alosa sapidissima Introduced I M AN IID E USA pp Mylopharodon Hardhead Native O M F IC pp conocephalus Hybrid green/ Lepomis ssp. Introduced I M F IID - bluegill Mirror carp Cyprinus carpio Introduced O T F IIE Europe pp Lampetra Pacific lamprey Native O T AN, F ID pp tridentata Pacific staghorn Leptocottus Native I M E,F IE pp sculpin armatus River lamprey Lampetra ayresi Native O M AN, F ID pp Shimofuri goby Tridentiger bifasciatus Introduced O M E IIE Japan pp Smallmouth Micropterus bass dolomieui Introduced I/P M F IID M USA pp Speckled dace (Sacramento) Rhinichthys osculus carringtoni Native I T F IE pp Threespine Gasterostreus stickleback aculeatus Native O M AN, E, F IE pp Tule perch Hysteocarpus traski Native I I E,F ID pp Turtle, pond - Yellowfin goby Acanthogobius flavimanus Introduced O M F IID E Asia pp Totals 18,426 Data source: California Department of Fish and Game. Community Assessment of Fish Caught By CDFG 19 Mar Dec 2011 (34 trips) Abbreviations Trophic Level: Tolerance to Degradation: Status*: O: omnivorous (includes omnivores, herbivores, general planktivores) I: invertivore (includes invertivores, zooplanktivores I/P: carnivore (includes piscivores, large invertebrates (crayfish), amphibian, and mammalian predators I: intolerant Life Style*: AM: amphidromous M: moderately tolerant AN: anadromous T: Tolerant E: estuarine resident F: freshwater resident I. Native species A. Extinct/extirpated B. Threatened or endangered C. Special concern D. Watch list E. Stable of increasing *Adapted from Moyle, Peter, Inland Fishes of California. University of California Press. Berkeley, California.

175 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 173 TABLE 2c. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT HILLS FERRY (SITE H) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Mosquitofish Gambusia affinis Introduced I T F IIE E USA pp ,017 Shrimp species Introduced O M E,F IIE 1,163 Carp Cyprinus carpio Introduced O T F IIE Europe pp White catfish Ameiurus catus Introduced I/P T F IID E USA pp Red shiner Cyprinella lutrensis Introduced O T F IIE M USA pp Inland silverside Menidia beryllina Introduced I M F IIE SE USA pp Bluegill Lepomis macrochirus Introduced I T F IID M USA pp Goldfish Carrrassius auratus Introduced O T F IID Japan pp Largemouth bass Micropterus salmoides Introduced P T F IID M USA pp Threadfin shad Dorosama petenese Introduced I M F IID SE USA pp Spotted bass Redear sunfish Micropterus punctulatus Lepomis microlophus Introduced P M F IIE SE USA pp Introduced I M F IID SE USA pp Channel catfish Ictalurus punctatus Introduced I/P M F IID M USA pp Green sunfish Lepomis cyanellus Introduced I/P T F IID M USA pp Striped bass Morone saxatilis Introduced P M AN IID E USA pp Red crayfish Fathead minnow Bigscale logperch Black crappie Procambarus (Scapulicambarus) clarkii Pimephales promelas Percina macrolepida Pomoxis nigromaculatus Introduced O T F IIE 48 Introduced O T F IIE M USA pp Introduced I T F IID SW USA pp Introduced I/P M F IID M USA pp Sacramento Sucker Catostomus occidentalis Native O M F IF pp Sacramento Blackfish microlepidotus Orthodon Native O T F IE pp Bullfrog Rana catesbeiana Introduced O T IIE 18 Smallmouth bass Micropterus dolomieui Introduced I/P M F IID M USA pp Tule perch Hysteocarpus traski Native I I E,F ID pp Notemigonus Golden shiner Introduced I M F IIE E USA pp crysoleucas Pogonichthys Sacramento Splittail Native O M E,F IB pp macrolepidotus Prickly sculpin Cottus asper Native I M AM,E,F IE pp Sacramento Pikeminnow grandis Ptychocheilus Native I/P M F IE pp Riffle sculpin Cottus gulosus Native I M F ID pp White crappie Pomoxis annularis Introduced I/P T F IID M USA pp Green x Redear Lepomis ssp. Introduced I/P T F IID M USA pp Bluegill x Redear Introduced I T F IID M USA pp Chinook Salmon Oncorhynchus tshawytscha Native I I AN, F IB pp Mirror Carp Cyprinus carpio Introduced O T F IIE Europe pp Turtle, pond Introduced O 1 Warmouth Lepomis gulosus Introduced I M F IIC M USA pp American shad Alosa sapidissima Introduced I M AN IID E USA pp

176 174 GRASSLAND BYPASS PROJECT TABLE 2c. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT HILLS FERRY (SITE H) (CONT.) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Black bullhead Ameiurus melas Introduced I/P T F IID E USA pp Brown bullhead Ameiurus nebulosus Hesperoleucus Introduced I/P T F IID M USA pp California roach symmetricus Native I M F ID pp symmetricus Green sunfish/bluegill Hybrid - Mylopharodon Hardhead Native O M F IC pp conocephalus Hitch Lavinia exilicauda Native O M F ID pp Pacific lamprey Lampetra tridentata Native O T AN, F ID pp Pacific Staghorn Leptocottus sculpin armatus Native I M E,F IE pp Pumpkin Seed Lepomis gibbosus Introduced I T F IID pp River lamprey Lampetra ayresi Native O M AN, F ID pp Shimofuri goby Tridentiger bifasciatus Introduced O M E IIE Japan pp Snail sp. Introduced O - Speckled dace (Sacramento) carringtoni Rhinichthys osculus Native I T F IE pp Threespine stickleback aculeatus Gasterostreus Native O M AN, E, F IE pp Acanthogobius Yellowfin goby Introduced O M F IID E Asia pp flavimanus Totals 14,943 Data source: California Department of Fish and Game. Community Assessment of Fish Caught By CDFG 19 Mar Dec 2011 (34 trips) Abbreviations Trophic Level: O: omnivorous (includes omnivores, herbivores, general planktivores) I: invertivore (includes invertivores, zooplanktivores I/P: carnivore (includes piscivores, large invertebrates (crayfish), amphibian, and mammalian predators Tolerance to Degradation: I: intolerant Life Style*: AM: amphidromous M: moderately tolerant AN: anadromous T: Tolerant E: estuarine resident F: freshwater resident Status*: I. Native species A. Extinct/extirpated B. Threatened or endangered C. Special concern D. Watch list E. Stable of increasing *Adapted from Moyle, Peter, Inland Fishes of California. University of California Press. Berkeley, California.

177 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 175 TABLE 2d. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT HILLS FERRY (SITE H) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Mosquitofish Gambusia affinis Introduced I T F IIE E USA pp ,162 Shrimp species Introduced O M E,F IIE 1,110 Carp Cyprinus carpio Introduced O T F IIE Europe pp White catfish Ameiurus catus Introduced I/P T F IID E USA pp Red shiner Cyprinella lutrensis Introduced O T F IIE M USA pp Bluegill Lepomis macrochirus Introduced I T F IID M USA pp Inland silverside Menidia beryllina Introduced I M F IIE SE USA pp Goldfish Carrrassius auratus Introduced O T F IID Japan pp Largemouth bass Micropterus salmoides Introduced P T F IID M USA pp Threadfin shad Dorosama petenese Introduced I M F IID SE USA pp Spotted bass Micropterus punctulatus Introduced P M F IIE SE USA pp Redear sunfish Lepomis microlophus Introduced I M F IID SE USA pp Channel catfish Ictalurus punctatus Introduced I/P M F IID M USA pp Green sunfish Lepomis cyanellus Introduced I/P T F IID M USA pp Striped bass Morone saxatilis Introduced P M AN IID E USA pp Fathead minnow Red crayfish Bigscale logperch Pimephales promelas Introduced O T F IIE M USA pp Procambarus (Scapulicambarus) clarkii Introduced O T F IIE 36 Percina macrolepida Introduced I T F IID SW USA pp Black crappie Pomoxis nigromaculatus Introduced I/P M F IID M USA pp Sacramento Sucker Catostomus occidentalis Native O M F IF pp Sacramento Orthodon Blackfish microlepidotus Native O T F IE pp Bullfrog Rana catesbeiana Introduced O T IIE 18 Tule perch Hysteocarpus traski Native I I E,F ID pp Smallmouth bass Micropterus dolomieui Introduced I/P M F IID M USA pp Golden shiner Notemigonus crysoleucas Introduced I M F IIE E USA pp Sacramento Splittail Pogonichthys macrolepidotus Native O M E,F IB pp Prickly sculpin Cottus asper Native I M AM,E,F IE pp Sacramento Pikeminnow Ptychocheilus grandis Native I/P M F IE pp Riffle sculpin Cottus gulosus Native I M F ID pp White crappie Pomoxis annularis Introduced I/P T F IID M USA pp Green x Redear Lepomis ssp. Introduced I/P T F IID M USA pp Bluegill x Redear Introduced I T F IID M USA pp Chinook Salmon Oncorhynchus tshawytscha Native I I AN, F IB pp Mirror Carp Cyprinus carpio Introduced O T F IIE Europe pp Turtle, pond Introduced O 1 Warmouth Lepomis gulosus Introduced I M F IIC M USA pp American shad Alosa sapidissima Introduced I M AN IID E USA pp Black bullhead Ameiurus melas Introduced I/P T F IID E USA pp Brown bullhead Ameiurus nebulosus Introduced I/P T F IID M USA pp California roach Hesperoleucus symmetricus symmetricus Native I M F ID pp

178 176 GRASSLAND BYPASS PROJECT TABLE 2d. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT HILLS FERRY (SITE H) (CONT.) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Green sunfish/ Bluegill Hybrid - Hardhead Mylopharodon conocephalus Native O M F IC pp Hitch Lavinia exilicauda Native O M F ID pp Pacific lamprey Lampetra tridentata Native O T AN, F ID pp Pacific Staghorn sculpin Leptocottus armatus Native I M E,F IE pp Pumpkin Seed Lepomis gibbosus Introduced I T F IID pp River lamprey Lampetra ayresi Native O M AN, F ID pp Shimofuri goby Tridentiger bifasciatus Introduced O M E IIE Japan pp Snail sp. Introduced O - Speckled dace Rhinichthys osculus (Sacramento) carringtoni Native I T F IE pp Threespine stickleback Yellowfin goby Gasterostreus aculeatus Native O M Acanthogobius flavimanus AN, E, F IE pp Introduced O M F IID E Asia pp Totals 12,839 Data source: California Department of Fish and Game. Community Assessment of Fish Caught By CDFG 19 Mar Dec 2011 (34 trips) Abbreviations Trophic Level: O: omnivorous (includes omnivores, herbivores, general planktivores) I: invertivore (includes invertivores, zooplanktivores I/P: carnivore (includes piscivores, large invertebrates (crayfish), amphibian, and mammalian predators Tolerance to Degradation: Status*: I: intolerant Life Style*: AM: amphidromous M: moderately tolerant AN: anadromous T: Tolerant E: estuarine resident F: freshwater resident I. Native species A. Extinct/extirpated B. Threatened or endangered C. Special concern D. Watch list E. Stable of increasing *Adapted from Moyle, Peter, Inland Fishes of California. University of California Press. Berkeley, California.

179 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 177 TABLE 2e. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT CHINA ISLAND (SITE R) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Mosquitofish Gambusia affinis Introduced I T F IIE E USA pp ,855 Red shiner Cyprinella lutrensis Introduced O T F IIE M USA pp Shrimp species Introduced O M E,F IIE 53 Inland silverside Menidia beryllina Introduced I M F IIE SE USA pp Red crayfish Procambarus (Scapulicambarus) clarkii Introduced O T F IIE 12 Smallmouth bass Micropterus dolomieui Introduced I/P M F IID M USA pp Threadfin shad Largemouth bass Dorosama petenese Introduced I M F IID SE USA pp Micropterus salmoides Introduced P T F IID M USA pp Bluegill Lepomis macrochirus Introduced I T F IID M USA pp Carp Cyprinus carpio Introduced O T F IIE Europe pp White catfish Ameiurus catus Introduced I/P T F IID E USA pp Goldfish Carrrassius auratus Introduced O T F IID Japan pp Spotted bass Redear sunfish Green sunfish Channel catfish Micropterus punctulatus Introduced P M F IIE SE USA pp Lepomis microlophus Introduced I M F IID SE USA pp Lepomis cyanellus Introduced I/P T F IID M USA pp Ictalurus punctatus Introduced I/P M F IID M USA pp Striped bass Morone saxatilis Introduced P M AN IID E USA pp Fathead minnow Pimephales promelas Introduced O T F IIE M USA pp Black crappie Pomoxis nigromaculatus Introduced I/P M F IID M USA pp Sacramento Sucker Bigscale logperch Sacramento Blackfish Catostomus occidentalis Native O M F IF pp Percina macrolepida Introduced I T F IID SW USA pp Orthodon microlepidotus Native O T F IE pp Bullfrog Rana catesbeiana Introduced O T IIE - Tule perch Hysteocarpus traski Native I I E,F ID pp Sacramento Splittail Pogonichthys macrolepidotus Native O M E,F IB pp Prickly sculpin Cottus asper Native I M AM,E,F IE pp Sacramento Pikeminnow Ptvychocheilus grandis Native I/P M F IE pp Golden shiner Notemigonus crysoleucas Introduced I M F IIE E USA pp Green x Redear Lepomis ssp. Introduced I M F IID - Bluegill x Redear - Chinook Salmon Oncorhynchus tshawytscha Native I I AN, F IB pp Mirror Carp Cyprinus carpio Introduced O T F IIE Europe pp Turtle, pond - Warmouth Lepomis gulosus Introduced I M F IIC M USA pp American shad Alosa sapidissima Introduced I M AN IID E USA pp Black bullhead Brown bullhead California roach Ameiurus melas Introduced I/P T F IID E USA pp Ameiurus nebulosus Introduced I/P T F IID M USA pp Hesperoleucus symmetricus symmetricus Native I M F ID pp

180 178 GRASSLAND BYPASS PROJECT TABLE 2e. COMMUNITY ASSESSMENT OF FISH CAUGHT BY CDFG SAN JOAQUIN RIVER AT CHINA ISLAND (SITE R) (CONT.) COMMON NAME SCIENTIFIC NAME ORIGIN TROPHIC TOLERANCE TO DEGRADATION LIFE STYLE* STATUS* FROM MOYLE REFERENCE TOTAL SAMPLES Hardhead Mylopharodon conocephalus Native O M F IC pp Hitch Lavinia exilicauda Native O M F ID pp Pacific lamprey Lampetra tridentata Native O T AN, F ID pp Pacific Staghorn sculpin Leptocottus armatus Native I M E,F IE pp Pumpkin Seed Lepomis gibbosus Introduced I T F IID pp Riffle sculpin Cottus gulosus Native I M F ID pp River lamprey Lampetra ayresi Native O M AN, F ID pp Shimofuri goby Tridentiger bifasciatus Introduced O M E IIE Japan pp Snail sp. Introduced O - Speckled dace (Sacramento) Threespine stickleback Rhinichthys osculus carringtoni Native I T F IE pp Gasterostreus aculeatus Native O M AN, E, F IE pp White crappie Pomoxis annularis Introduced I/P T F IID M USA pp Yellowfin goby Acanthogobius flavimanus Introduced O M F IID E Asia pp Totals 2,104 Data source: California Department of Fish and Game. Community Assessment of Fish Caught By CDFG 19 Mar Dec 2009 (33 trips) Abbreviations Trophic Level: Tolerance to Degradation: Status*: O: omnivorous (includes omnivores, herbivores, general planktivores) I: invertivore (includes invertivores, zooplanktivores I/P: carnivore (includes piscivores, large invertebrates (crayfish), amphibian, and mammalian predators I: intolerant Life Style*: AM: amphidromous M: moderately tolerant AN: anadromous T: Tolerant E: estuarine resident F: freshwater resident I. Native species A. Extinct/extirpated B. Threatened or endangered C. Special concern D. Watch list E. Stable of increasing *Adapted from Moyle, Peter, Inland Fishes of California. University of California Press. Berkeley, California.

181 CHAPTER 7b: BIOLOGICAL EFFECTS OF THE GRASSLANDS BYPASS PROJECT AT SITES E, G, H, AND R 179

182 180 GRASSLAND BYPASS PROJECT

183 08 TOXICITY CHAPTER 8: TOXICITY TESTING FOR THE GRASSLAND BYPASS PROJECT TESTING FOR THE GRASSLAND BYPASS PROJECT 181 Chris Linneman 1 1 Summers Engineering The objective of the laboratory toxicity testing is to evaluate the potential toxicity of water-borne contaminants within the Grassland Bypass Project (GBP) area using standardized bioassay protocols conducted under controlled environmental conditions. The laboratory toxicity tests evaluate one species within each of three trophic levels using short-term chronic testing procedures (7 or 4 days) and lethal (survival) and non-lethal (growth or reproduction) endpoints (USEPA 1987; 1994). The test species are Selenastrum capricornutum (alga), Daphnia magna (water flea), and Pimephales promelas (fathead minnow). The testing is not specific for any single chemical exposure, but rather demonstrates the net effect of only waterborne contaminant exposures in the site waters on the selected test species. During toxicity testing, test species are fed a controlled diet that is unrelated to field sources of food. For this reason, toxicity testing is not expected to detect selenium toxicity in invertebrates and fish because the main route of exposure in these groups of organisms is through the food they eat. However, selenium toxicity in algae is through direct exposure from water and thus toxicity testing may detect selenium toxicity in algae. Tests are conducted at the screening level, comparing the ambient water to 100% test water. If significant toxicity is observed, definitive tests (dilution series) may be conducted. Water samples are collected from Stations B, C, D, and F for each monthly testing period. The Delta-Mendota Canal (DMC) station is the control site. Additionally, selenium concentrations were determined from water samples collected for each toxicity testing event by the U.S. Bureau of Reclamation (USBR) contract laboratories. However, in-situ chronic toxicity testing using caged fathead minnows has been eliminated during the course of the program, as well as measurement of selenium bioaccumulation in algae. In September of 2012 a reduction in the toxicity sampling frequency occurred. Sampling events were changed from monthly to quarterly. The change in sampling frequency was a decision made by the DCRT upon review of past toxicity data. The new toxicity sampling plan will be reflected in the revised 2015 Grassland Bypass Monitoring Plan. continuted on next page >

184 182 GRASSLAND BYPASS PROJECT SUMMARY. The toxicity program for 2012 was conducted by Block Environmental Service s (BES) Bioassay Laboratory Division under the guidance of the San Luis and Delta-Mendota Water Authority. Technical assistance, quality assurance/ quality control (QA/QC), and program oversight is provided by the USBR. The toxicity program in 2012 collected samples on a monthly basis and samples were collected in all months except for October and December. A summary of the 2012 toxicity data is included in Tables 2012-A, 2012-B, 2012-C. A list of results that exhibited statistically significant toxicity during 2012 are included in Table 1. TABLE 1: 2012 SUMMARY OF TOXIC SAMPLES SITE SAMPLE DATE SPECIES % SURVIVAL MEAN GROWTH MEAN REPRODUCTION Site B 5/14/2012 Daphnia Magna 90 NA 33 Site C 7/9/2012 Daphnia Magna 20 NA 24.1 Site D 7/9/2012 Daphnia Magna 40 NA 36.4 Site B 8/6/2012 Daphnia Magna 40 NA 10.2 Site F 9/17/2012 Daphnia Magna 80 NA 18.2 Site F 2/6/2012 Selenastrum Capricornutum NA 4.94 NA Site B 3/5/2012 Selenastrum Capricornutum NA NA Site D 3/5/2012 Selenastrum Capricornutum NA NA Site C 5/14/2012 Selenastrum Capricornutum NA 8.25 NA Site B 9/17/2012 Selenastrum Capricornutum NA NA Site B 11/26/2012 Selenastrum Capricornutum NA NA Site D 11/26/2012 Selenastrum Capricornutum NA NA 2013 SUMMARY. The toxicity program for 2013 was conducted by Block Environmental Service s (BES) Bioassay Laboratory Division under the guidance of the San Luis and Delta-Mendota Water Authority. Technical assistance, quality assurance/quality control (QA/QC), and program oversight is provided by the USBR. Toxicity samples were collected in March and June of 2013, after which, BES ended its environmental toxicity testing services. A summary of the 2013 toxicity data is included in Table 2013-A. A list of results that exhibited statistically significant toxicity during 2013 are included in Table 2 below. TABLE 2: 2013 SUMMARY OF TOXIC SAMPLES SITE SAMPLE DATE SPECIES % SURVIVAL MEAN GROWTH MEAN REPRODUCTION Site D 6/3/2013 Pimephales Promelas 88 NA NA Site B 3/13/2013 Selenastrum Capricornutum NA NA Site F 3/13/2013 Selenastrum Capricornutum NA 19.2 NA

185 CHAPTER 8: TOXICITY TESTING FOR THE GRASSLAND BYPASS PROJECT SUMMARY. The toxicity program for 2014 was conducted by Pacific Ecorisk (PER) under the guidance of the San Luis and Delta- Mendota Water Authority. Technical assistance, quality assurance/quality control (QA/QC), and program oversight is provided by the USBR. Toxicity samples were collected in March and June and September of A summary of the 2014 toxicity data is included in Tables 2014-A, 2014-B, and 2014-C. A list of results that exhibited statistically significant toxicity during 2014 are included in Table 3 below. TABLE 3: 2014 SUMMARY OF TOXIC SAMPLES SITE SAMPLE DATE SPECIES % SURVIVAL MEAN GROWTH MEAN REPRODUCTION Conductivity Control 6/10/2014 Daphnia Magna 60 NA 32.8 Site D 6/10/2014 Daphnia Magna 90 NA 53.1 Site F 6/10/2014 Daphnia Magna 20 NA 41.7 Conductivity Control 9/16/2014 Daphnia Magna 0 NA 0 Site B 9/16/2014 Daphnia Magna 0 NA 0 Site B 9/16/2014 Pimephales Promelas NA Site F 9/16/2014 Pimephales Promelas NA Site B 3/18/2014 Selenastrum Capricornutum NA 4.19 NA Site B 6/10/2014 Selenastrum Capricornutum NA 2.18 NA Site B 9/16/2014 Selenastrum Capricornutum NA 1.29 NA Conductivity Control 6/10/2016 Selenastrum Capricornutum NA 2.94 NA Site B 6/10/2016 Selenastrum Capricornutum NA 2.18 NA Site D 6/10/2016 Selenastrum Capricornutum NA 2.82 NA Site F 6/10/2016 Selenastrum Capricornutum NA 5.39 NA

186 184 GRASSLAND BYPASS PROJECT

187 09 SEDIMENT CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 185 Michael C. S. Eacock1 Jeffrey E. Papendick 2 Harry Horner3 Brian Urbick4 1 Project Manager/Soil Scientist, U.S. Bureau of Reclamation, Mid-Pacific Region, South-Central California Area Office, Fresno, California meacock@usbr.gov. 2 Natural Resources Technician, U.S. Bureau of Reclamation, South-Central California Area Office, 1243 N Street, Fresno, California jpapendick@usbr.gov 3 Physical Scientist, U.S. Bureau of Reclamation, Mid Pacific Region, Sacramento, California hhorner@usbr.gov 4 Physical Scientist, U.S. Bureau of Reclamation, Mid Pacific Region, Sacramento, California burbick@usbr.gov This chapter presents the measurements of selenium in sediments in the San Luis Drain, Mud Slough, and Salt Slough. The Grassland Bypass Project conveys agricultural drainage water in the Drain to Mud Slough, a tributary of the San Joaquin River in central California. The Project has removed this drainage water from more than 93 miles of water supply channels, including Salt Slough, which delivers clean water to local wetlands and wildlife refuges. PURPOSE Sediment monitoring for the Grassland Bypass Project focuses on measuring selenium and organic carbon in the San Luis Drain (SLD), Mud Slough, and Salt Slough. The purpose of the monitoring is to assess the changes in selenium concentrations in the sediment during the project. The measurements within the SLD provide selenium concentration estimates for comparison with California Department of Health Services hazardous waste criterion. The measurements in Mud and Salt Slough provide selenium concentrations for comparison with US Fish and Wildlife Service thresholds for ecological risk. ECOLOGICAL RISK GUIDELINES (FOR MUD AND SALT SLOUGH) Based on a review of 27 studies, Van Derveer and Canton 5 concluded that sedimentary selenium is a reliable predictor of adverse biological effects and that a preliminary toxic threshold existed at about 2.5 mg/kg (dry weight) for the 10th percentile for effects. They also noted that, in the literature they reviewed, adverse effects were always observed at selenium concentrations greater than 4.0 mg/kg (dry weight) in sediments 6. For this report, the ecological risk guidelines for selenium concentrations in sediment are as follows: no effect - less than 2 mg/kg, dry weight, level of concern - 2 to 4 mg/kg, dry weight toxic - greater than 4 mg/kg, dry weight. 5 Van Derveer, W. D. and S. Canton Selenium sediment toxicity thresholds and derivation of water quality criteria for freshwater biota of western stream. Environ. Toxicol. Chem. 16: National Irrigation Water Quality Program, November Information Report No. 3 - Guidelines for Interpretation of the Biological Effects of Selected Constituents in Biota, Water, and Sediment.

188 186 GRASSLAND BYPASS PROJECT Hazardous Waste Criteria (for the San Luis Drain) The State of California 7 has established a characteristic of toxicity for hazardous waste containing selenium with a concentration of 100 mg/kg (wet weight) 8. Should the selenium concentrations in sediment from the San Luis Drain exceed this value, the sediment would be considered a hazardous material. Any material dredged from the drain would have to be deposited in a hazardous waste site. Sampling Locations Sampling locations for sediment monitoring were located at Site C - Mud Slough upstream of the SLD discharge Site D - Mud Slough downstream of the SLD discharge Site I2 - a backwater in Mud Slough below the SLD discharge Site E - Mud Slough at Highway 140 Site F - Salt Slough at Highway 165 (Lander Ave) Twenty locations in the SLD were selected based on a probability sampling scheme associated with the amount of sediment estimated within each check. The estimated cubic yards for each check came from the annual survey made each year by the San Luis & Delta-Mendota Water Authority. Sampling Frequency Sediment samples were collected three times in 2012, twice in 2013, and four times in Samples of sediment are collected from twenty places along the San Luis Drain each year. SAMPLING METHODS Mud and Salt Sloughs Sediment samples were collected using an acrylic coring device (4.5 cm diameter, 38 cm internal length). After collecting the sediment, sections of the core, 0-3 cm and 3-8 cm, were slowly extruded using a non metallic internal pushing device and placed in distinct quart sized mixing bowls. An additional sample was collected near the same spot for the whole core sample and placed into a third mixing bowl. The process was repeated at two other points across the slough. Materials from the second and third samples were placed in the corresponding 0-3 cm, 3-8 cm and whole core mixing bowls containing the first samples. Each of the mixing bowls contains material from the transect. The 0-3 cm, 3-8 cm, and whole core samples were then mixed well in their mixing bowls in a manner similar to kneading bread. The mixing objective was to obtain one homogeneous sample in each of the bowls. San Luis Drain Only 8 cm whole core samples were collected in the San Luis Drain. Composite samples were then placed in a wide mouth polyethylene container and stored in an ice chest at 4oC. Results Tables 1 through 7 show the results of sediment analysis of whole core samples collected from 1996 through 2014 from Mud Slough and Salt Slough. All values are based on dry weight. Tables 8, 9, and 10 list the concentration of selenium in sediment along the San Luis Drain in 2012, 2013, and The values are listed dry and wet weights. 7 California Code of Regulations. Title 22. Division 4.5. Chapter 11. Article (a)(2)(a) Table II List of Inorganic Persistent and Bioaccumulative Toxic Substances and their Soluble and Total Threshold Limit Concentration Values 8 Wet weight (mg/kg) = dry weight (mg/kg)* (1 percent moisture/100)

189 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 187 Figures 1 and 2 depict the concentration of selenium at stations A and B in the San Luis Drain. Figures 3 through 7 depict the selenium concentration is sediments in Mud and Salt Sloughs. Figure 8 depicts the concentration of selenium in sediments samples collected at locations in the San Luis Drain. Ecological Risk: Mud and Salt Slough Selenium concentrations in the sediment from Mud Slough (Sites C, D, and E) and Salt Slough (Site F) continue to be below the 2.0 mg/kg (dry weight) no effect level for all samples collected during 2012 and The results are listed in Tables 3, 4, 5, 6 and 7, and shown in Figures 3, 4, 5, 6 and 7. Hazardous Waste Criteria: San Luis Drain Results from the annual in-drain surveys for 2012 through 2014 are depicted in Tables 8, 9, and 10. In general, the concentration of selenium in sediment tends to be higher at the north end of the drain, particularly between Checks 1 and 4. During the 2012 sampling period, the highest concentration was near Check 3 with a result of 10.2 mg/kg, wet weight. In 2013, the highest concentration was measured at the same location but slightly lower 7.2 mg/kg, wet weight. In 2014, the highest concentration was at the terminus at Mud Slough with a value of 7.2 mg/kg, wet weight. These results are well below the hazardous waste criteria of 100 mg/kg, wet weight. The formula for converting dry weigh to wet weight is as follows: Tables wet weight = (dry weight mg Se/kg) * (1.0 - percent moisture/100). Table 1. San Luis Drain (GBP Station A) Sediment Monitoring Results Table 2. San Luis Drain near terminus (GBP Station B) Sediment Monitoring Results Table 3. Mud Slough above SLD discharge (GBP Station C): Sediment Monitoring Results Table 4. Mud Slough below SLD discharge (GBP Station D): Sediment Monitoring Results Table 5. Mud Slough at Highway 140 (GBP Station E): Sediment Monitoring Results Table 6. Salt Slough at Highway 165 (GBP Station F): Sediment Monitoring Results Table 7. Mud Slough backwater (GBP Stations I and I2): Sediment Monitoring Results Table 8. Annual sediment sampling in the San Luis Drain, June 2012 Table 9. Annual sediment sampling in the San Luis Drain, September 2013 Table 10. Annual sediment sampling in the San Luis Drain, June 2014 Figures Figure 1. Selenium in Sediment in the San Luis Drain (GBP Station A) Figure 2. Selenium in Sediment at the San Luis Drain Terminus (GBP Station B) Figure 3. Selenium in Sediment in Mud Slough above the SLD Discharge (GBP Station C) Figure 4. Selenium in Sediment in Mud Slough below the SLD Discharge (GBP Station D) Figure 5. Selenium in Sediment in Mud Slough below the SLD Discharge (GBP Station E) Figure 6. Selenium in Sediment in Salt Slough (GBP Station F) Figure 7. Selenium in Sediment in Mud Slough Backwater below SLD Discharge (GBP Stations I and I2) Figure 8. Concentration of Selenium (mg/kg wet weight) in Sediment in the San Luis Drain

190 188 GRASSLAND BYPASS PROJECT TABLE 1. SAN LUIS DRAIN (STATION A) SEDIMENT MONITORING RESULTS SAMPLING DATE SELENIUM CONCENTRATION WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT ORGANIC CARBON WHOLE CORE % PERCENT MOISTURE WHOLE CORE % Feb Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Jun Jul Jun Jun Jun Jul Jun Jun Jun Nov Jun Sep Jun Summary Data: March Present Maximum Minimum Median Average Count Notes:

191 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 189 TABLE 2. SAN LUIS DRAIN NEAR TERMINUS (STATION B) SEDIMENT MONITORING RESULTS SAMPLING DATE SELENIUM CONCENTRATION WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT ORGANIC CARBON WHOLE CORE % PERCENT MOISTURE WHOLE CORE % Feb Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Jul Jun Jun Jun Jul Jun Jun Jun Nov Mar Jun Sep Mar Sep Mar Jun Sep Nov Summary Data: June Present Maximum Minimum Median Average Count

192 190 GRASSLAND BYPASS PROJECT TABLE 3. MUD SLOUGH ABOVE DRAINAGE DISCHARGE (STATION C): SEDIMENT MONITORING RESULTS SAMPLING DATE MG/KG, DRY WEIGHT SELENIUM CONCENTRATION WHOLE CORE MG/KG, WET WEIGHT ORGANIC CARBON WHOLE CORE % PERCENT MOISTURE WHOLE CORE % Mar May Jun Sep Nov Mar Jun < Sep Nov Mar Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Nov Mar < Jun Nov Mar Jun Sep Nov < Mar Jun < Sep < Nov < Apr Jun < Sep Dec Mar Jun < Sep Nov Mar < Jun Sep Nov Mar < Jun < Aug < Nov < Mar < Jun < Sep < Dec

193 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 191 TABLE 3. MUD SLOUGH ABOVE DRAINAGE DISCHARGE (STATION C): SEDIMENT MONITORING RESULTS (CONT.) SAMPLING DATE MG/KG, DRY WEIGHT SELENIUM CONCENTRATION WHOLE CORE MG/KG, WET WEIGHT ORGANIC CARBON WHOLE CORE % PERCENT MOISTURE WHOLE CORE % Mar Nov Mar Jun Sep Mar Sep Mar Jun Sep Nov Summary Data: May Present Maximum Minimum Median Average Count

194 192 GRASSLAND BYPASS PROJECT TABLE 4. MUD SLOUGH BELOW DRAINAGE DISCHARGE (STATION D): SEDIMENT MONITORING RESULTS SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Mar Apr < Jun Sep Nov Mar Jun Sep Nov Mar NA NA NA NA Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Nov Mar < Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Apr NA NA NA NA Jun Sep Dec Mar Jun Sep NA 0.23 NA Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun < Sep Dec

195 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 193 TABLE 4. MUD SLOUGH BELOW DRAINAGE DISCHARGE (STATION D): SEDIMENT MONITORING RESULTS (CONT.) SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Mar Nov Mar Jun Sep Mar Sep Mar Jun Sep Nov Summary Data: May Present Maximum Minimum Median Average Count

196 194 GRASSLAND BYPASS PROJECT TABLE 5. MUD SLOUGH AT HIGHWAY 140 (STATION E): SEDIMENT MONITORING RESULTS SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Mar May Jun < Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Apr Jun Sep Dec Mar Jun Sep na 0.38 n/a Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Dec Mar

197 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 195 TABLE 5. MUD SLOUGH AT HIGHWAY 140 (STATION E): SEDIMENT MONITORING RESULTS (CONT) SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Nov Mar Jun Sep < Mar Sep Mar Jun Sep Nov Summary Data: May Present Maximum Minimum Median Average Count

198 196 GRASSLAND BYPASS PROJECT TABLE 6. SALT SLOUGH AT HIGHWAY 165 (STATION F): SEDIMENT MONITORING RESULTS SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Feb Jun Sep Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Apr Jun Sep Dec Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Aug Nov Mar Jun Sep Dec Mar Nov

199 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 197 TABLE 6. SALT SLOUGH AT HIGHWAY 165 (STATION F): SEDIMENT MONITORING RESULTS (CONT.) SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Mar Jun Sep Mar Sep Mar Jun Sep Nov Summary Data: June Present Maximum Minimum Median Average Count

200 198 GRASSLAND BYPASS PROJECT TABLE 7. MUD SLOUGH BACKWATER (STATION I AND I2): SEDIMENT MONITORING RESULTS SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Jun Mar Jun Jun Mar Jun Nov Mar Jun Aug Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Nov Apr Jun Sep Dec Mar Jun Sep n/a Nov Mar Jun Sep Nov Mar Jun Sep Nov Mar Jun Sep Dec Mar Nov Mar Jun Sep Mar Sep Mar Jun Sep Nov

201 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 199 TABLE 7. MUD SLOUGH BACKWATER (STATION I AND I2): SEDIMENT MONITORING RESULTS (CONT.) SAMPLING DATE WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT WHOLE CORE % WHOLE CORE % Summary Data: June Present Maximum Minimum Median Average Count

202 200 GRASSLAND BYPASS PROJECT TABLE 8. ANNUAL SEDIMENT SAMPLING IN THE SAN LUIS DRAIN, JUNE 2012 VOLUME SURVEY RESULTS SEDIMENT ANALYSIS (5) OCTOBER 2012 JUNE 2012 SAN LUIS DRAIN CHECKNUMBER SAN LUIS DRAIN MILE POST LANDMARK MILES BETWEEN CHECKS ESTIMATED CUBIC YARDS CY/MILE SAMPLING DATE (1) (4) SELENIUM CONCENTRATION WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT TOTAL ORGANIC CARBON WHOLE CORE PERCENT MOISTURE WHOLE CORE % % Terminus at Mud Slough 6/6/ M south of terminus 6/6/ Station B Check 1/Gun Club Road ,981 4, M south of Check 1 6/6/ Check 2/Hwy ,771 7, M south of Check 2 6/6/ Check ,881 13, M South of Check 3 6/6/ M north of Check 4 6/6/ Check ,711 6, M north of Check 5 6/6/ Check 5/Wolfsen Road ,741 11, Check ,593 7, mile north of Check 7 6/6/ Check ,403 7, M south of Check Check 8/Henry Miller Road ,282 7, M south of Check 8 6/6/ Check 9/Santa Fe Canal ,471 9, M south of Check 9 6/6/ Check 10/Hwy ,369 6, M south of Check 10 6/6/ M south of Check 10 6/6/ M south of Check 10 6/6/ Check ,629 7, Check ,766 17, M south of Check 12 6/7/ M south of Check 12' 6/7/ Check 13/Sierra Gun Club Rd ,572 16, M south of Check 13 6/7/ Check ,878 18, M south of Check 14 6/7/ M south of Check 14 6/7/ Check 15/Torchina Grade ,128 18, M south of Check 15 6/7/ Check ,089 18, M south of Check 16 6/7/ Check ,838 13, Check 18/Aqua Vista Rd ,968 8, Station A M south of Check 18 6/7/ Check 19/Russell Avenue ,229 6,228 Total ,300 Notes: Sediment volume and distribution measured by San Luis and Delta-Mendota Water Authority All samples collected by the US Bureau of Reclamation, Sacramento CA All samples analyzed by the Cal Dept Fish and Game Lab, Rancho Cordova CA (Selenium & Percent moisture) and CLS, Rancho Cordova CA (Total organic carbon) Wet Weight =dry weight concentration x (1 - (percent moisture/100))

203 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 201 TABLE 9. ANNUAL SEDIMENT SAMPLING IN THE SAN LUIS DRAIN, 2013 VOLUME SURVEY RESULTS SEDIMENT ANALYSIS (5) JANUARY 2014 SEPTEMBER 2013 SAN LUIS DRAIN CHECKNUMBER SAN LUIS DRAIN MILE POST LANDMARK MILES BETWEEN CHECKS ESTIMATED CUBIC YARDS CY/MILE SAMPLING DATE (1) (4) SELENIUM CONCENTRATION WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT TOTAL ORGANIC CARBON WHOLE CORE PERCENT MOISTURE WHOLE CORE % % M south of Check 1 9/25/ Check 2/Hwy ,430 9, M south of Check 2 9/25/ Check ,019 14, M South of Check 3 9/25/ M north of Check Check ,579 7, M north of Check 5 9/25/ Check 5/Wolfsen Road ,105 11, Check ,695 7, Check ,547 7, M south of Check 7 9/25/ Check 8/Henry Miller Road ,838 8, M south of Check 8 9/25/ Check 9/Santa Fe Canal ,983 10, M south of Check 9 9/25/ Check 10/Hwy ,196 7, M south of Check 10 9/26/ M south of Check 10 9/26/ M south of Check 10 9/26/ Check ,413 7, Check ,443 18, M south of Check 12 9/26/ M south of Check 12' 9/26/ Check 13/Sierra Gun Club Rd ,747 16, M south of Check 13 9/26/ Check ,503 18, M south of Check 14 9/26/ M south of Check 14 9/26/ Check 15/Torchina Grade ,884 17, M south of Check 15 9/26/ Check ,240 17, M south of Check 16 9/26/ Check ,104 12, Check 18/Aqua Vista Rd ,238 7, Station A 9/26/ M south of Check 18 9/26/ Check 19/Russell Avenue ,154 5,313 Total ,467 Notes: Sediment volume and distribution measured by San Luis and Delta-Mendota Water Authority All samples collected by the US Bureau of Reclamation, Sacramento CA t All samples analyzed by the Cal Dept Fish and Game Lab, Rancho Cordova CA (Selenium & Percent moisture) and CLS, Rancho Cordova CA (Total organic carbon) Wet Weight =dry weight concentration x (1 - (percent moisture/100))

204 202 GRASSLAND BYPASS PROJECT TABLE 10. ANNUAL SEDIMENT SAMPLING IN THE SAN LUIS DRAIN, 2014 SAN LUIS DRAIN CHECKNUMBER SAN LUIS DRAIN MILE POST LANDMARK MILES BETWEEN CHECKS VOLUME SURVEY RESULTS SEDIMENT ANALYSIS (5) JANUARY 2014 JUNE 2014 ESTIMATED CUBIC YARDS CY/MILE SAMPLING DATE (1) (4) SELENIUM CONCENTRATION WHOLE CORE MG/KG, DRY WEIGHT MG/KG, WET WEIGHT TOTAL ORGANIC CARBON WHOLE CORE PERCENT MOISTURE WHOLE CORE % % M south of Check 1 6/26/ Check 2/Hwy ,430 9, M south of Check 2 6/26/ Check ,019 14, M South of Check 3 6/26/ M north of Check Check ,579 7, M north of Check 5 6/26/ Check 5/Wolfsen Road ,105 11, Check ,695 7, Check ,547 7, M south of Check Check 8/Henry Miller Road ,838 8, M south of Check 8 6/26/ Check 9/Santa Fe Canal ,983 10, M south of Check 9 6/26/ Check 10/Hwy ,196 7, M south of Check 10 6/25/ M south of Check 10 6/25/ M south of Check 10 6/25/ Check ,413 7, Check ,443 18, M south of Check 12 6/25/ M south of Check /25/ ' Check 13/Sierra Gun ,747 16,841 Club Rd M south of Check 13 6/25/ Check ,503 18, M south of Check 14 6/25/ M south of Check 14 6/25/ Check 15/Torchina Grade ,884 17, M south of Check 15 6/25/ Check ,240 17, M south of Check Check ,104 12, Check 18/Aqua Vista Rd ,238 7, Station A 6/25/ M south of Check 18 6/25/ Check 19/Russell Avenue ,154 5,313 Total ,467 Notes: Sediment volume and distribution measured by San Luis and Delta-Mendota Water Authority All samples collected by the US Bureau of Reclamation, Sacramento CA All samples analyzed by the Cal Dept Fish and Game Lab, Rancho Cordova CA (Selenium & Percent moisture) and CLS, Rancho Cordova CA (Total organic carbon) Wet Weight =dry weight concentration x (1 - (percent moisture/100))

205 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 203 FIGURE 1. SELENIUM IN SEDIMENT IN THE SAN LUIS DRAIN (GBP STATION A) Selenium Concentration (mg Se/kg, wet weight) mg/kg Hazardous Waste Threshold 10 0 Feb-96 Mar-96 Jun-96 Sep-96 Nov-96 Mar-97 Jun-97 Sep-97 Nov-97 Mar-98 Jun-98 Sep-98 Nov-98 Feb-99 Jun-99 Sep-99 Nov-99 Mar-00 Jun-00 Sep-00 Nov-00 Mar-01 Jun-01 Jun-02 Jul-03 Jun-04 Jun-05 Jun-06 Jul-07 Jun-08 Jun-09 Jun-10 Nov-11 Jun-12 Sep-13 Jun-14 FIGURE 2. SELENIUM IN SEDIMENT AT THE SAN LUIS DRAIN TERMINUS (GBP STATION B) Selenium Concentration (mg Se/kg, wet weight) mg/kg Hazardous Waste Threshold Feb-96 Mar-96 Jun-96 Sep-96 Nov-96 Mar-97 Jun-97 Sep-97 Nov-97 Mar-98 Jun-98 Sep-98 Nov-98 Feb-99 Jun-99 Sep-99 Nov-99 Mar-00 Jun-00 Sep-00 Nov-00 Mar-01 Jun-02 Jul-03 Jun-04 Jun-05 Jun-06 Jul-07 Jun-08 Jun-09 Jun-10 Nov-11 Mar-12 Jun-12 Sep-12 Mar-13 Sep-13 Mar-14 Jun-14 Sep-14 Nov-14

206 204 GRASSLAND BYPASS PROJECT FIGURE 3. SELENIUM IN SEDIMENT IN MUD SLOUGH ABOVE THE SLD DISCHARGE (GBP STATION C) mg/kg threshold of concern Mar-96 Jun-96 Nov-96 Jun-97 Nov-97 Jun-98 Nov-98 Jun-99 Nov-99 Jun-00 Nov-00 Jun-01 Nov-01 Jun-02 Nov-02 Jun-03 Mar-04 Sep-04 Mar-05 Sep-05 Apr-06 Sep-06 Mar-07 Sep-07 Mar-08 Sep-08 Mar-09 Aug-09 Mar-10 Sep-10 Mar-11 Mar-12 Sep-12 Sep-13 Jun-14 Nov-14 Selenium Concentration (mg Se/kg, dry weight) FIGURE 4. SELENIUM IN SEDIMENT IN MUD SLOUGH BELOW THE SLD DISCHARGE (GBP STATION D) mg/kg threshold of concern 1.8 Selenium Concentration (mg Se/kg, dry weight) Mar-96 Jun-96 Nov-96 Jun-97 Nov-97 Jun-98 Nov-98 Jun-99 Nov-99 Jun-00 Nov-00 Jun-01 Nov-01 Jun-02 Nov-02 Jun-03 Nov-03 Jun-04 Nov-04 Jun-05 Nov-05 Jun-06 Dec-06 Jun-07 Nov-07 Jun-08 Nov-08 Jun-09 Nov-09 Jun-10 Dec-10 Nov-11 Jun-12 Mar-13 Mar-14 Sep-14

207 CHAPTER 9: SEDIMENT MONITORING IN THE SAN LUIS DRAIN, MUD AND SALT SLOUGHS 205 FIGURE 5. SELENIUM IN SEDIMENT IN MUD SLOUGH BELOW THE SLD DISCHARGE (GBP STATION E) mg/kg threshold of concern 1.8 Selenium Concentration (mg Se/kg, dry weight) Mar-96 Jun-96 Nov-96 Jun-97 Nov-97 Jun-98 Nov-98 Jun-99 Nov-99 Jun-00 Nov-00 Jun-01 Nov-01 Jun-02 Nov-02 Jun-03 Nov-03 Jun-04 Nov-04 Jun-05 Nov-05 Jun-06 Dec-06 Jun-07 Nov-07 Jun-08 Nov-08 Jun-09 Nov-09 Jun-10 Dec-10 Nov-11 Jun-12 Mar-13 Mar-14 Sep-14 FIGURE 6. SELENIUM IN SEDIMENT IN SALT SLOUGH (GBP STATION F) mg/kg threshold of concern 1.8 Selenium Concentration (mg Se/kg, dry weight) Mar Sep Mar Sep Mar Sep Feb Sep Mar Sep Mar Aug Mar Sep Mar Sep Mar Sep Mar Sep Apr Sep Mar Sep Mar Sep Mar Aug Mar Sep Mar Mar Sep Sep Jun Nov

208 206 GRASSLAND BYPASS PROJECT FIGURE 7. SELENIUM IN SEDIMENT IN MUD SLOUGH BACKWATER BELOW SLD DISCHARGE (GBP STATIONS I AND I2) 10 Site I Site I Selenium Concentration (mg Se/kg, dry weight) mg/kg threshold of toxicity 2 mg/kg threshold of concern 0 Jun-96 Mar-97 Jun-98 Jun-99 Mar-00 Jun-01 Nov-00 Mar-01 Jun-01 Aug-01 Nov-01 Mar-02 Jun-02 Sep-02 Nov-02 Mar-03 Jun-03 Sep-03 Nov-03 Mar-04 Jun-04 Sep-04 Nov-04 Mar-05 Jun-05 Sep-05 Nov-05 Apr-06 Jun-06 Sep-06 Dec-06 Mar-07 Jun-07 Sep-07 Nov-07 Mar-08 Jun-08 Sep-08 Nov-08 Mar-09 Jun-09 Sep-09 Nov-09 Mar-10 Jun-10 Sep-10 Dec-10 Mar-11 Nov-11 Mar-12 Jun-12 Sep-12 Mar-13 Sep-13 Mar-14 Jun-14 Sep-14 Nov-14 FIGURE 8. CONCENTRATION OF SELENIUM (MG/KG WET WEIGHT) IN SEDIMENT IN THE SAN LUIS DRAIN Station A (Milepost 105) 100 mg/kg hazardous waste threshold Direction of Flow ==========> Station B (Milepost 79) Selenium concentration in sediment (mg/kg wet weight) San Luis Drain Mile Post

209 10 SEDIMENT CHAPTER 10: SEDIMENT QUANTITY IN THE SAN LUIS DRAIN QUANTITY IN THE SAN LUIS DRAIN 207 Joseph C. McGahan1 1 Drainage Coordinator. INTRODUCTION The purpose of this aspect of the Grassland Bypass Monitoring Program (Monitoring Program) is to determine the changes in quantity and movement of sediment in the San Luis Drain (SLD). This is accomplished by actual measurement of the bed sediment and using total suspended solids measurements at the inlet and outlet of the SLD. SEDIMENT QUANTITY MONITORING PROCEDURE Section 11.4 of the Compliance Monitoring Program Phase II (USBR et al., 2001) describes the procedure to measure the quantity of sediment in the SLD. The Monitoring Program calls for the measurement of sediment in four reaches of the SLD (Reaches 1, 10, 14, and 17). The locations of the sediment measurement points duplicated those of the March of 1987 survey performed by Summers Engineering. San Luis & Delta-Mendota Water Authority Personnel performed the sediment surveys in October of 2012, January 2014 and October The sediment bed was cross-sectioned at regular intervals in all 19 reaches of the SLD, with depth-to-sediment measurements taken at both banks and in the middle of the channel. These three measurements were used to calculate an average volume of sediment per foot of channel, which was then used to estimate the total volume of sediment in the SLD from Check 19 to the outlet at Mud Slough (North). Table 1a, Table 1b, Table 1c and Table 1d summarize the results from 1987 through the 2014 survey. Note that, due to schedule conflicts, the 2013 survey was completed approximately 3 months later (in January 2014) than typical for previous years. The results are also shown graphically in Figure 1a and Figure 1b Survey: For 2012, the results indicate a net decrease of 1,172 cubic yards from November of 2011 to October of 2012, amounting to a less than 1% change from The accuracy of measurement of the sediment is well outside of this 1% apparent increase. Although the measuring protocol is consistent, the density and resolution of measurements is inadequate to capture small changes in volume. An estimated total of 192,000 cubic yards of sediment have accumulated in the SLD since July During the 2012 period Pool 11 gained the largest volume of sediment, approximately 4,500 cubic yards. The 2012 average depth of sediment measured 3.8 feet with the maximum depth of 7.5 feet measured in Pool 15. Sediment accumulation is generally occurring in the upstream quarter (Pools 9 through 13, about 5,035 cubic yards) of the drain Survey: For 2013, the results measured an increase of 8,168 cubic yards from October 2012 to January 2014 (approximately 545 cubic yards per month). Pool 11 once again gained the largest sediment volume at approximately 3,676 additional cubic yards Survey: For 2014, the results measured a decrease of 5,981 cubic yards from January 2014 to October 2014, amounting to a 2% reduction in measured volume. As noted earlier, this small change in volume is beyond the resolution of the estimate method. Flows through the San Luis Drain in 2014 were the lowest recorded since the start of the Grassland Bypass project 87% less than the 1996 discharge at the start of the Grassland Bypass Project and 30% less than the 2013 discharge which may have caused shrinkage in new exposed sediment beds as the sediment dries out. An estimated total of 194,000 cubic yards of sediment have accumulated in the SLD since July 1998.

210 208 GRASSLAND BYPASS PROJECT TOTAL SUSPENDED SOILDS MEASUREMENTS The Monitoring Program calls for total suspended solids (TSS) measurements as part of the water quality monitoring. These measurements were to be taken just downstream of the inlet to the SLD (Site A) and just upstream of the outlet (Site B). Measurements were taken on a weekly basis at these sites. The monthly averages are shown for WY 1997 through December 2014 in Table 2a, 2b, and 2c. Overall, the data shows that TSS concentrations at Site A are higher than at Site B by a factor of 1.8:1 for 2012, by 2.1:1 for 2013, and 1.7:1 for 2014 (averaged over the 12 month period). One commitment of the Monitoring Program was to minimize flows so as to not cause sediment movement or suspension of sediments from the bottom of the SLD. The data suggests that the suspended sediments are settling in the SLD and that there is no net movement or suspension of sediments. References U.S. Bureau of Reclamation et al Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project, Phase II, March U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, CA. U.S. Bureau of Reclamation et al Compliance Monitoring Program for Use and Operation of the Grassland Bypass Project, September U.S. Bureau of Reclamation, Mid-Pacific Region, Sacramento, CA. Tables Table 1a. San Luis Drain Sediment Survey 1987 to 2000 Survey Summary and Comparison Table 1b San Luis Drain Sediment Survey 2001 to 2005 Survey Summary and Comparison Table 1c. San Luis Drain Sediment Survey 2006 to 2010 Survey Summary and Comparison Table 1d. San Luis Drain Sediment Survey 2011 to 2014 Survey Summary and Comparison Table 2a - Total Suspended Solids to 2004 Table 2b - Total Suspended Solids to 2012 Table 2c. Total Suspended Solids (Monthly Average) to 2014 Figures Figure 1a. San Luis Drain Sediment Survey Comparison Figure 1b. San Luis Drain Sediment Survey Comparison

211 CHAPTER 10: SEDIMENT QUANTITY IN THE SAN LUIS DRAIN 209 TABLE 1a. SAN LUIS DRAIN SEDIMENT SURVEY 1987 TO 2000 SURVEY SUMMARY AND COMPARISON March 1987 June-Sept July 1998 July 1999 August 2000 Pool Checks Distance Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile (miles) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) End End to ,176 1,203 1, ,795 1,059 3,602 1,364 4,451 1,686 1* 1 to ,567 1,410 1,840 1,011 3,375 1,854 4,514 2,480 5,306 2, to ,059 3, , , , , to ,909 1,910 3,350 1,304 4,839 1,883 3,244 1,262 5,582 2, to ,440 2,467 6,521 3,623 9,049 5,027 6,760 3,756 8,968 4, to ,242 2,059 4,370 2,121 4,596 2,231 4,139 2,009 5,679 2, to ,160 2,602 2,584 3,113 2,432 2,930 1,762 2,123 2,416 2, to ,935 8,744 3,278 7,285 3,135 6,967 3,099 6,887 3,068 6, to , , , ,334 1,420 3, to ,963 2,176 6,390 1,997 8,571 2,678 4,632 1,448 8,797 2,749 10* 10 to ,647 1,813 2,708 1,855 2,781 1,905 3,101 2,124 3,669 2, to ,835 1,934 4,947 1,979 7,620 3,048 6,499 2,600 10,194 4, to , ,977 1,504 3, ,367 2,274 4, to ,038 2,240 1,771 1,946 2,657 2,920 2,709 2,977 3,835 4,215 14* 14 to ,304 1,719 3,803 2,838 5,427 4,050 12,030 8,978 11,466 8, to ,822 1,898 2,700 2,813 6,456 6,725 11,699 12,186 15,420 16, to ,863 3,490 7,605 4,527 10,482 6,239 12,895 7,676 14,691 8,745 17* 17 to ,885 2,772 3,006 4,420 2,435 3,581 3,205 4,713 3,477 5, to ,558 1,607 1,768 1,822 2,519 2,597 2,603 2,684 2,819 2,906 Totals Averages * Required by Grassland Bypass Monitoring Program ,094 60,594 82,406 88, ,368 2,145 2,238 3,370 3,741 4,744 TABLE 1b SAN LUIS DRAIN SEDIMENT SURVEY 2001 TO 2005 SURVEY SUMMARY AND COMPARISON November 2001 November 2002 October 2003 December 2004 October 2005 Pool Checks Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) End End to 1 5,611 2,125 6,338 2,401 8,595 3,256 9,498 3,598 9,290 3,519 1* 1 to 2 5,487 3,015 7,661 4,209 7,993 4,392 9,258 5,087 9,535 5, to 3 1,748 6,242 2,496 8,914 2,219 7,924 2,719 9,711 3,269 11, to 4 6,404 2,492 9,349 3,638 9,301 3,619 11,567 4,501 12,847 4, to 5 9,836 5,465 11,496 6,387 12,522 6,956 15,244 8,469 15,662 8, to 6 6,481 3,146 7,765 3,770 8,710 4,228 10,945 5,313 11,088 5, to 7 2,321 2,797 3,530 4,253 3,891 4,688 4,822 5,809 4,613 5, to 8 2,842 6,315 2,990 6,644 2,851 6,335 2,987 6,637 2,657 5, to 9 1,600 3,404 1,775 3,776 2,050 4,361 2,382 5,068 2,355 5, to 10 9,364 2,926 10,420 3,256 12,306 3,846 12,820 4,006 10,878 3,399 10* 10 to 11 3,835 2,626 4,975 3,408 5,791 3,967 6,279 4,301 6,295 4, to 12 10,900 4,360 13,692 5,477 16,099 6,440 17,099 6,840 17,179 6, to 13 1,966 4,273 2,324 5,052 2,454 5,336 2,806 6,100 2,943 6, to 14 4,378 4,811 5,884 6,466 6,965 7,653 8,530 9,373 11,346 12,468 14* 14 to 15 14,917 11,132 18,720 13,970 21,788 16,260 25,335 18,907 27,518 20, to 16 18,661 19,438 19,214 20,015 19,126 19,923 19,675 20,495 19,435 20, to 17 21,132 12,578 20,971 12,483 21,209 12,624 21,947 13,064 22,236 13,236 17* 17 to 18 4,900 7,206 5,318 7,821 5,446 8,009 5,275 7,757 5,443 8, to 19 3,427 3,533 3,571 3,681 4,039 4,164 3,804 3,922 3,936 4,058 Totals Averages * Required by Grassland Bypass Monitoring Program 135, , , , ,527 5,678 6,612 7,052 7,840 8,185

212 210 GRASSLAND BYPASS PROJECT TABLE 1c. SAN LUIS DRAIN SEDIMENT SURVEY 2006 TO 2010 SURVEY SUMMARY AND COMPARISON October 2006 October 2007 October 2008 November 2009 October 2010 Pool Checks Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) End End to 1 9,811 3,716 11,013 4,171 11,425 4,328 10,975 4,157 11,978 4,537 1* 1 to 2 10,070 5,533 10,555 5,799 11,164 6,134 11,888 6,532 12,965 7, to 3 3,585 12,803 3,852 13,758 3,408 12,172 3,516 12,558 3,823 13, to 4 12,990 5,055 14,133 5,499 14,679 5,712 16,050 6,245 15,700 6, to 5 16,920 9,400 18,293 10,163 17,459 9,699 18,676 10,376 18,673 10, to 6 13,413 6,511 12,965 6,294 12,423 6,030 12,809 6,218 13,129 6, to 7 5,297 6,382 5,040 6,072 4,894 5,897 5,289 6,372 5,750 6, to 8 3,040 6,756 2,860 6,356 2,721 6,047 3,073 6,828 3,407 7, to 9 3,051 6,490 3,120 6,638 3,376 7,184 3,891 8,279 4,343 9, to 10 13,535 4,230 14,496 4,530 14,393 4,498 16,376 5,118 18,193 5,685 10* 10 to 11 8,389 5,746 8,386 5,744 8,816 6,038 9,413 6,447 10,072 6, to 12 20,537 8,215 21,596 8,638 23,540 9,416 30,654 12,262 35,751 14, to 13 3,966 8,622 5,144 11,182 5,678 12,343 7,004 15,227 7,192 15, to 14 12,041 13,232 12,597 13,843 18,169 19,966 18,220 20,022 18,616 20,457 14* 14 to 15 28,179 21,029 27,917 20,834 24,833 18,532 23,658 17,655 24,083 17, to 16 19,598 20,414 19,216 20,016 18,240 19,000 17,411 18,136 17,422 18, to 17 22,750 13,541 21,750 12,946 23,636 14,069 22,225 13,229 22,403 13,335 17* 17 to 18 5,120 7,529 5,447 8,011 6,161 9,060 6,462 9,503 6,401 9, to 19 3,583 3,694 3,645 3,758 4,038 4,163 4,120 4,247 3,954 4,076 Totals 215, , , , ,852 Averages 8,889 9,171 9,489 9,969 10,412 * Required by Grassland Bypass Monitoring Program TABLE 1d. SAN LUIS DRAIN SEDIMENT SURVEY 2011 TO 2014 SURVEY SUMMARY AND COMPARISON November 2011 October 2012 January 2014 October 2014 Total since 1997 Pool Checks Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume Vol / mile Volume (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) (cu yd/mi) (cu yd) End End to 1 17,177 6,507 11,981 4,538 12,351 4,678 13,190 4,996 11,493 1* 1 to 2 17,220 9,462 13,771 7,566 16,430 9,028 15,403 8,463 13, to 3 4,255 15,198 3,881 13,860 4,019 14,352 3,652 13,044 3, to 4 19,088 7,427 17,711 6,892 19,579 7,618 18,795 7,313 15, to 5 21,184 11,769 20,741 11,523 21,105 11,725 19,977 11,098 13, to 6 14,400 6,990 14,593 7,084 14,695 7,134 14,481 7,030 10, to 7 6,341 7,639 6,403 7,714 6,547 7,888 6,521 7,856 3, to 8 3,614 8,031 3,282 7,294 3,838 8,530 3,665 8, to 9 4,869 10,360 4,471 9,513 4,983 10,602 5,028 10,698 4, to 10 22,214 6,942 21,369 6,678 23,196 7,249 23,751 7,422 17,361 10* 10 to 11 10,406 7,127 10,629 7,280 11,413 7,817 11,467 7,854 8, to 12 39,213 15,685 43,766 17,507 47,442 18,977 46,252 18,501 41, to 13 7,091 15,415 7,572 16,460 7,747 16,842 7,578 16,474 6, to 14 16,255 17,863 16,878 18,547 16,503 18,135 16,283 17,893 14,512 14* 14 to 15 22,907 17,095 24,128 18,006 23,884 17,824 23,520 17,552 19, to 16 17,117 17,830 18,089 18,842 17,240 17,958 16,577 17,267 13, to 17 21,819 12,988 22,838 13,594 21,104 12,562 20,166 12,003 12,561 17* 17 to 18 5,853 8,607 5,968 8,776 5,238 7,703 5,202 7,650 2, to 19 4,447 4,585 6,229 6,421 5,154 5,313 4,979 5,133 3,211 Totals 275, , , , ,892 Averages 10,922 10,952 11,154 10,863 * Required by Grassland Bypass Monitoring Program

213 CHAPTER 10: SEDIMENT QUANTITY IN THE SAN LUIS DRAIN 211 TABLE 2a - TOTAL SUSPENDED SOLIDS TO 2004 (Monthly Average) Site A Site B Site A Site B Date TSS TSS Date TSS TSS mg/l mg/l mg/l mg/l Oct Oct Nov Nov Dec Dec Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept WY 1997 Average WY 2001 Average Oct Oct Nov Nov Dec Dec Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept WY 1998 Average Oct Oct Nov Nov Dec Dec CY 2002 Average Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept WY 1999 Average Oct Oct Nov Nov Dec Dec CY 2003 Average Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept WY 2000 Average Oct Nov G:\data\SPRDSHTS\GRASLAND\MONITOR\Drnarea\SLD\[Sed_Tables14.xls]Table 2 Dec CY 2004 Average

214 212 GRASSLAND BYPASS PROJECT TABLE 2b - TOTAL SUSPENDED SOLIDS TO 2012 (Monthly Average) Site A Site B Site A Site B Date TSS TSS Date TSS TSS mg/l mg/l mg/l mg/l Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept Oct Oct Nov Nov Dec Dec CY 2005 Average CY 2009 Average Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept Oct Oct Nov Nov Dec Dec CY 2006 Average CY 2010 Average Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept Oct Oct Nov Nov Dec Dec CY 2007 Average CY 2011 Average Jan Jan Feb Feb Mar Mar Apr Apr May May Jun Jun Jul Jul Aug Aug Sept Sept Oct Oct Nov Nov Dec Dec CY 2007 Average CY 2012 Average

215 CHAPTER 10: SEDIMENT QUANTITY IN THE SAN LUIS DRAIN 213 TABLE 2c. TOTAL SUSPENDED SOLIDS (MONTHLY AVERAGE) TO 2014 Site A Site B Date TSS TSS mg/l mg/l Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec CY 2013 Average Jan Feb Mar Apr May Jun Jul Aug Sep Oct. 14 NA 86 Nov. 14 NA 74 Dec. 14 NA 49 CY 2014 Average

216 214 GRASSLAND BYPASS PROJECT FIGURE 1a. SAN LUIS DRAIN SEDIMENT SURVEY COMPARISON 25,000 20,000 15,000 Cubic Yards/Mile 10,000 5,000 0 End 1* * * * 18 Pool * Required by GBP 1987 Survey (Summers Eng.) 1997 Survey (SLDMWA) 1998 Survey (SLDMWA) 1999 Survey (SLDMWA) 2000 Survey (SLDMWA) 2001 Survey (SLDMWA) 2002 Survey (SLDMWA) 2003 Survey (SLDMWA) 2004 Survey (SLDMWA) FIGURE 1b. SAN LUIS DRAIN SEDIMENT SURVEY COMPARISON 25,000 20,000 Cubic Yards/Mile 15,000 10,000 5,000 0 End 1* * * * 18 * Required by GBP Monit. Program. Pool 1987 Survey (Summers Eng.) 2005 Survey (SLDMWA) 2006 Survey (SLDMWA) 2007 Survey (SLDMWA) 2008 Survey (SLDMWA) 2009 Survey (SLDMWA) 2010 Survey (SLDMWA) 2011 Survey (SLDMWA) 2012 Survey (SLDMWA) 2013 Survey (SLDMWA) 2014 Survey (SLDMWA0

217 11 QUALITY ASSURANCE CHAPTER 11: QUALITY ASSURANCE 215 Christopher Garduño1 1 Quality Assurance Specialist, U.S. Bureau of Reclamation, Mid Pacific Region, Sacramento, California cgarduno@usbr.gov DATA QUALITY OBJECTIVES The Data Collection and Reporting Team (DCRT) use the laboratory data from this project to support the determination as to whether selenium levels in the Grassland Bypass exceed regulatory compliance levels. Because individuals use the data generated by this program for regulatory compliance and baseline monitoring purposes, the data must be of the highest degree of validity. Sample collection of different environmental media and analytical methods performed by the laboratories must adhere to the guidelines established in the Quality Assurance Project Plan (QAPP). QUALITY ASSURANCE PROJECT PLAN On August 22, 2002, the U.S. Bureau of Reclamation (USBR) and the DCRT completed and released the QAPP for Phase II of the use and operation of the Grassland Bypass Project (GBP). USBR initiated a review and revision of the QAPP in The QAPP was reviewed and revised from 2005 through 2006; an updated version was issued November 20, The QAPP provides the protocols for documenting the Quality Assurance/Quality Control (QA/QC) activities carried out by the agencies responsible for the separate components of the Compliance Monitoring Program (CMP II). The QAPP describes the organization and membership of the project participants and defines the data quality objectives (DQOs) for CMP II. This plan describes the QA/QC activities associated with each agency s monitoring program, provides the QA/QC protocol of each laboratory participating in the program, provides acceptance criteria for data validation procedures, and describes corrective actions to be taken when the data fail to meet such criteria. The QAPP addresses both quantitative goals, including precision, accuracy, and completeness, and qualitative goals, including representativeness and comparability. The QAPP follows the format described in the May 1994 Guidelines for Preparing Quality Assurance Project Plans, published by the State of California Department of Water Resources. The QAPP includes all the requirements identified in the August 1994 Draft Interim Final, U.S. EPA Requirements for Quality Assurance Project Plans for Environmental Data Operations, EPA QA/R-5. The QAPP will be updated and revised when a new Waste Discharge Requirement (WDR) is issued. The new Waste Discharge Requirement was tentatively scheduled to be enacted in October As of May 2015, the WDR has not been finalized.

218 216 GRASSLAND BYPASS PROJECT Quality Assurance Oversight QA/QC oversight for CMP II is the responsibility of a QA/QC oversight manager (QAQCOM) working for USBR. The QAQCOM oversees the implementation of commitments, guidelines, practices, and protocols outlined in the QAPP in compliance with the goals and objectives of the project. The QAQCOM uses guidelines, protocols, and criteria established in the QAPP to monitor and validate data collected by USBR personnel and to audit the data collection and validation processes used by the other participating agencies, including the U.S. Environmental Protection Agency (EPA), U.S. Fish and Wildlife Service (USFWS), U.S. Geological Survey (USGS), California Department of Fish and Game (CDFG), California Regional Water Quality Control Board (CRWQCB), and San Luis Delta- Mendota Water Authority (SLDMWA). When the QAQCOM identifies a noncompliance issue, the appropriate QA Officer is notified, and the responsible agency implements corrective actions to resolve the problem. The QAQCOM brings any unresolved issues between the QAQCOM and a participating agency s QA Officer to the attention of the DCRT for resolution. USBR QA personnel conduct audits of all participating analytical laboratories and review the data collection activities of the participating agencies for adherence to protocol. Additionally, USBR QA personnel conduct field audits on agencies participating in CMP II by evaluating sampling methods in the field. Laboratory Performance and System Audits During 2012, 2013 and 2014, USBR conducted performance and system audits on laboratories that perform work in support of the Grassland Bypass Project (Table 1 and Table 2). The laboratories performed well and provided acceptable corrective actions for any deficiencies noted during the audits. Laboratories are audited by USBR every three to four years. The audit consists of performing a documentation review, submitting performance evaluation (PE) samples to the laboratory, and conducting an on-site system audit of the laboratory. Documentation Review Prior to the audit, the laboratory s QA Manual and a copy of the last three years of approved round-robin performance study results are reviewed. Any deficiencies in the QA manual, performance study results, or corrective actions for unacceptable values on PE samples are addressed in the audit report. Performance Evaluation Samples Prior to the on-site audit, PE samples are submitted by USBR to the laboratories for a more direct evaluation of the laboratory s performance. The purpose of the PE samples is to evaluate the laboratory s ability to generate accurate data. The parameters selected for the PE samples correspond to those analyzed by the laboratories in support of the Grassland Bypass Project. Unacceptable PE sample results are addressed in the audit report. The results of the PE samples submitted by USBR to the laboratories are presented in Table 2. On-Site System Audit An on-site system audit is conducted to assess the laboratory s expertise in performing sample analyses, their capability for producing valid data, their ability to effectively support the data, and the integrity of their QA/QC practices. During the on-site audit, the QA Officer, analysts, and other key laboratory personnel are questioned to determine their overall understanding of the methods and laboratory procedures. Documentation practices are also reviewed. In general, the auditors are ensuring that laboratory procedures follow the laboratory s QA manual guidelines and the analytical method protocols. Any deviations are addressed in the audit report. Audit Report The auditors send a report identifying deficiencies found during the audit to the laboratory with a time frame for the laboratory to respond to the findings and to implement and document the corrective actions.

219 CHAPTER 11: : QUALITY ASSURANCE 217 Sample Collection System Audits The sample collection system audits focus on the quality of the environmental samples collected and the ability of field personnel to adequately support and document the sample collection process. The purpose of the sample collection system audits is to identify and prevent problems in the field that could compromise sample integrity. On August 08-09, 2012, USBR conducted a field audit of Stacy Brown who collects samples in support of the Grassland Bypass Project. All aspects of the sample collection process were audited including equipment calibration and use, equipment decontamination, sample collection protocol, and documentation practices. Any deviations were addressed in the audit report. Data Validation and Review Audit The QAQCOM is responsible for ensuring the participating agencies properly validated their analytical data, identified problems, and contacted their respective laboratories to initiate corrective actions. The QAQCOM is also responsible for ensuring the participating agencies properly calibrated their instruments and documented their field work. To accomplish this, USBR reviewed and audited the laboratory and field data generated by the participating agencies as discussed below. Any deviations from the QAPP were provided in writing to the agencies. Laboratory Data USBR did not audit other agency s laboratory data in 2012, 2013, or Most analytical work is handled by USBR. If other agency data is available, USBR will assess the validity of the analytical results by comparing QC sample results to acceptance criteria identified in Table 10 of the QAPP. The guidelines in the QAPP address both internal and external QC sample results. The QAPP defines internal QC samples as those check samples incorporated by the laboratories performing the work and defines external QC samples as those check samples submitted to the laboratories by the participating agencies. During the data review, validation, and audit process, USBR will perform the following: verify that agencies are correctly incorporating external QC samples (i.e., spikes, references, duplicates, blanks) into batches of field samples bring laboratory QC summary report issues to the attention of each agency s QA Officer check data packages to ensure laboratories are documenting the details of their corrective actions check to ensure the laboratories are analyzing project samples within required holding times identify possible outliers (analytical results that are outside of the established range) Field Data In August 2012, USBR personnel conducted an audit on field data generated by Stacy Brown and in September 2014, USBR personnel conducted two audits on field data generated by Terry Falaschi with Panoche Water District and Larry Marques with San Luis Delta Mendota Water Authority. These reviews were performed to ensure proper documentation was in place to support instrument calibration and sample collection procedures. Deficiencies were noted during the Panoche Water District audit that required a change in sample collectors from Panoche Water District to USBR at the Site A autosamplers. A review of the data at Site A after two months showed no significant change in data quality. Data Validation and Review Activities The following routine data validation, review, and audit activities were performed in 2012, 2013, and 2014 to ensure data validity as stated in the QAPP:

220 218 GRASSLAND BYPASS PROJECT TYPE OF DATA Laboratory and field data from USBR (sediment and water) Laboratory data from Block Environmental Services (water) Laboratory and field data from USFWS and CDFG(biota) REVIEW AND VALIDATION GROUP USBR Block Environmental Services USFWS QA ISSUES In September 2012, California Laboratory Services (CLS) notified USBR that they would no longer be able to perform total organic carbon analysis for the Grassland Bypass Project sediment samples due to instrument malfunction. They also stated it would not be possible to continue this analysis in the future. Samples were picked up from CLS and delivered to TestAmerica, Inc. TestAmerica analyzed one round of samples; however their reporting limit was higher than required. In an effort to find a laboratory with a lower reporting limit, a performance evaluation sample for total organic carbon was submitted to Calscience Environmental Laboratories, Inc. Calscience successfully analyzed the PE samples, meeting USBR s acceptance limits. In addition, Calscience s reporting limit for total organic carbon was acceptable. Samples requiring total organic carbon analysis will be submitted to Calscience. In 2012, South Dakota Agricultural Laboratories, the laboratory providing selenium analysis of water samples, changed facilities causing samples to become backlogged although no samples were held longer than their 6 month holding time. An on-site system audit was conducted at their new facility. In July of 2013, Block Environmental Services (BES) closed their bioassay testing section. BES was the laboratory responsible for water toxicity analysis for the Grassland Bypass Program. Pacific Ecorisk, an environmental toxicology laboratory in Fairfield, CA, will perform future water toxicity testing. USBR plans to audit and submit performance evaluation samples to Pacific Ecorisk in At the end of 2013, USBR performed an audit of the California Department of Fish and Wildlife Water Pollution Control Laboratory (CDFW-WPCL). A range of deficiencies were discovered, mostly affecting the legal defensibility of their data. It is important to note that CDFW-WPCL performed acceptably on the performance evaluation samples for selenium analysis on a variety of matrices (Table 2); selenium data analyzed by the CDFW-WPCL in support of the GBP should be regarded as accurate and valid. But due to a perceived lack of funding and staffing, it is USBR s assessment that CDFW-WPCL is incapable of producing highly defensible results on par with other contract laboratories from USBR s approved laboratory list. CDFW-WPCL will no longer analyze samples in support of the GBP. A field audit of Terry Falaschi with the Panoche Water District in September of 2014 collecting samples at Site A, determined that insufficient sample collection techniques were being followed. Sample collection responsibility was transferred to USBR personnel for the Site A Autosampler. At the end of 2014, USBR identified a possible site identification error being made by SLDMWA in collection of the Grassland Bypass Toxicity samples. The error was corrected, and a field audit was performed to ensure that proper sample collection techniques were being utilized. The same error occurred again in March of USBR facilitated coordination between the laboratory and SLDMWA to ensure the error would be eliminated. UNCERTAINTY ASSOCIATED WITH ENVIRONMENTAL MEASUREMENTS A degree of uncertainty accompanies all quantitative measurements. This is especially true for environmental data where measurement error may be introduced in the sample collection as well as in the laboratory preparation and analysis. Program participants and the public should understand that values presented in laboratory reports are not absolute, but rather represent values with associated precision and accuracy as defined in Table 10 of the QAPP. In addition, as the concentration of the parameter approaches the limit of detection for a particular analytical method, the level of uncertainty of the result increases significantly as shown in Figure 4 of the QAPP. The data user should understand the degree of uncertainty or the confidence limits associated with the data.

221 CHAPTER 11: : QUALITY ASSURANCE 219 SUMMARY In support of the Grassland Bypass project, USBR conducted audits of project laboratories and field personnel responsible for collecting samples. In addition, USBR validated, reviewed, and audited the data collected. USBR also performed comparison studies to find replacement laboratories for total organic carbon analysis in sediment samples and performed performance evaluation and system audits on South Dakota Agricultural Laboratories, Calscience Environmental Laboratories, Inc., and Block Environmental Services. In performing QA oversight, USBR seeks to ensure all participating agencies are operating in accordance with established QAPP protocols. Adherence to the QAPP ensures the reliability of the data collected and provides the necessary documentation to support the accuracy of the measurements. Tables Table 1. Laboratories Audited in 2012, 2013, and 2014 Table 2. Performance Evaluation Sample Results

222 220 GRASSLAND BYPASS PROJECT TABLE 1. LABORATORIES AUDITED IN 2012, 2013, AND 2014 LABORATORY AUDIT DATE(S) ANALYSIS TYPE FOR GBP South Dakota Ag. Laboratories Brookings, SD October 23-24, 2012 Selenium in water Block Environmental Pleasant Hill, CA September 26-27, 2012 Water toxicity Calscience Garden Grove, CA February 14-15, 2012 Total Organic Carbon in sediment WET Laboratory Sparks, NV Cal. Dept. Fish & Wildlife Pollution Control Laboratory Rancho Cordova, CA Pacific Ecorisk Fairfield, CA APPL Laboratory Clovis, CA California Laboratory Services Rancho Cordova, CA April 17-18, 2013 September 19-20, 2013 January 13 14, 2014 March 5-6, 2014 June 18-19, 2014 Metals and Nutrients in water Selenium in sediment and tissue Water toxicity Metals and Nutrients in water Total Suspended Solids in water

223 CHAPTER 11: : QUALITY ASSURANCE 221 TABLE 2. PERFORMANCE EVALUATION SAMPLE RESULTS SOUTH DAKOTA AGRICULTURAL LABORATORIES DATE: 9/25/2012 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA925 Water Selenium 1.73 µg/l 2.10 µg/l 82% 80% - 120% QA926 Water Selenium 9.53 µg/l 10.3 µg/l 93% 80% - 120% QA927 Water Selenium 98.8 µg/l 92 µg/l 107% 80% - 120% QA928 Water Selenium 1940 µg/l 1655 µg/l 117% 80% - 120% QA929 Tissue Selenium 1.42 mg/kg 1.63 mg/kg 87% 65% - 135% QA930 Sludge Selenium ND 0.44 mg/kg 0% 65% - 135% QA931 Vegetation Selenium mg/kg mg/kg 100% 65% - 135% DATE: 10/18/2012 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA937 Soil Selenium mg/kg 0.78 mg/kg 73% 65% - 135% QA938 Sludge Selenium 8.78 mg/kg 16.0 mg/kg 55% 65% - 135% QA938 - reanalysis Sludge Selenium 13.4 mg/kg 16.0 mg/kg 84% 65% - 135% QA939 Soil Selenium 1.22 mg/kg 1.52 mg/kg 80% 65% - 135% BLOCK ENVIRONMENTAL SERVICES DATE: 9/07/2012 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA919 Water Dissolved Oxygen 8.8 mg/l 8.62 mg/l 102% 80% - 120% QA920 Water Chlorine 1.22 mg/l 1.14 mg/l 107% 80% - 120% QA921 Water Hardness 366 mg/l 371 mg/l 99% 80% - 120% QA922 Water Alkalinity 82 mg/l 84.5 mg/l 97% 80% - 120% QA923 Water ph 8.1 s.u. 7.8 s.u. 104% 80% - 120% QA923 Water Conductivity 208 us/cm 214 us/cm 97% 80% - 120% QA924 Water Ammonia 3.0 mg/l 2.8 mg/l 104% 80% - 120% CALSCIENCE ENVIRONMENTAL LABORATORIES, INC. DATE: 11/16/2012 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA940 Soil TOC 3200 mg/kg 2520 mg/kg 127% 65%-135%

224 222 GRASSLAND BYPASS PROJECT TABLE 2. PERFORMANCE EVALUATION SAMPLE RESULTS (CONT.) WET LABORATORY DATE: 3/28/2013 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA953 Water Total Alkalinity 51 mg/l 50.4 mg/l 101% % QA954 QA956 Water Water Aluminum 2.5 mg/l 2.6 mg/l 96% % Barium 0.14 mg/l 0.14 mg/l 100% % Beryllium mg/l mg/l 92% % Boron 0.12 mg/l 0.15 mg/l - +/- RL (0.2 mg/l) Chromium mg/l mg/l 94% % Iron mg/l mg/l 94% % Manganese 0.37 mg/l 0.37 mg/l 100% % Molybdenum mg/l mg/l 91% % Nickel 1.0 mg/l 1.0 mg/l 100% % Silver mg/l mg/l 100% % Sodium 3.3 mg/l 2.8 mg/l 118% % Zinc 0.53 mg/l 0.51 mg/l 104% % Antimony mg/l mg/l 94% % Arsenic mg/l mg/l 98% % Cadmium mg/l mg/l 92% % Copper mg/l mg/l 100% % Lead mg/l mg/l 96% % Thallium mg/l mg/l 96% % Uranium 0.12 mg/l 0.13 mg/l 92% % Ammonia 0.52 mg/l 0.55 mg/l 95% % Total Phosphorous 0.70 mg/l 0.70 mg/l 100% % Nitrate + Nitrite 0.60 mg/l 0.60 mg/l 100% % CAL. DEPT. OF FISH & WILDLIFE WATER POLLUTION CONTROL LABORATORY DATE: 9/10/2013 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA1015 Tissue (Mussel) Selenium 1.86 mg/kg 1.8 mg/kg - +/- 2xRL QA1016 Sediment Selenium mg/kg 0.78 mg/kg 78% % QA1017 Biota (plankton) Selenium 1.68 mg/kg 1.75 mg/kg 96% % QA1018 Tissue (Fish) Selenium 3.64 mg/kg 3.56 mg/kg - +/- 2xRL

225 CHAPTER 11: : QUALITY ASSURANCE 223 TABLE 2. PERFORMANCE EVALUATION SAMPLE RESULTS (CONT.) APPL LABORATORY DATE: 2/12/2014 Sample ID Matrix Parameter Result True Value Percent Recovery Acceptance Limit QA1037 QA1038 Water Water Boron 198 ug/l 199 ug/l 99% Calcium 1950 ug/l 2000 ug/l 98% Iron 198 ug/l 199 ug/l 99% Magnesium 1980 ug/l 2000 ug/l 99% Potassium 3660 ug/l 3990 ug/l 92% Sodium 1880 ug/l 3990 ug/l 97% Aluminum 595 ug/l 598 ug/l 99% Antimony 10.9 ug/l 12 ug/l 91% Arsenic 11.4 ug/l 12 ug/l 95% Barium 31.7 ug/l 31.9 ug/l 99% Beryllium 6.2 ug/l 6.0 ug/l 103% Chromium 11.2 ug/l 12 ug/l 93% Manganese 82.6 ug/l 87.7 ug/l 94% Molybdenum 2.8 ug/l 3.0 ug/l 93% Nickel 221 ug/l 239 ug/l 92% Zinc 119 ug/l 120 ug/l 99% Bromide 1.7 mg/l 1.42 mg/l 120% Chloride 22.6 mg/l 23.6 mg/l 96% Fluoride 0.91 mg/l 0.96 mg/l 95% Sulfate 13 mg/l 14.6 mg/l 89% Alkalinity 48.8 mg/l 50.4 mg/l 97% TDS 119 mg/l 128 mg/l 93% 80% - 120% 80% - 120% QA1075 Water Mercury 4.3 ug/l 3.61 ug/l 119% 80% - 120% CALIFORNIA LABORATORY SERVICES DATE: 5/16/2014 QA1080 Water TSS 47 mg/l 51.2 mg/l 92% 80% - 120%

226 224 GRASSLAND BYPASS PROJECT

227 12 GRASSLAND CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW BYPASS PROJECT PEER REVIEW 225 Thomas Grieb, Ph.D.1 Harry Ohlendorf, Ph.D.2 David Janz, Ph.D.3 1 Environmental Health Science 2 Fish and Wildlife Ecology 3 Toxicology Compiled by the San Francisco Estuary Institute OVERALL INTRODUCTION The Grassland Bypass Project (GBP) manages and reduces the volume of agricultural drainwater and floodwater discharged from the 97,000-acre (44,000-hectare) Grassland Drainage Area (GDA) to the lower San Joaquin River and adjacent wetlands water supply channels. The Project is located in the Central Valley of California (Figure 1). The GBP includes a compliance monitoring project for tracking selenium, salt, boron, and other constituents in water, sediment, and biota throughout the study area (Figure 2). Data are reviewed by the interagency Data Collection and Review Team (DCRT) that consists of technical experts from the US Bureau of Reclamation (USBR), US Fish and Wildlife Service, US Environmental Protection Agency (USEPA), US Geological Survey, California Department of Fish and Wildlife, and the California Regional Water Quality Control Board. The GBP has been regulated by waste discharge requirements (WDRs) since The objective of the Project was to consolidate agricultural drainwater and floodwater generated in the GDA and divert these flows through the San Luis Drain, thus drastically reducing discharges into more sensitive areas. Various sites along the waterways now receiving the agricultural drainage, as well as several reference sites, are monitored regularly. The ultimate goal of the Project is to completely eliminate discharges of agricultural drainwater from the GDA by 2019 through highly conservative irrigation methods, reuse of water on salt-tolerant crops, and drainwater treatment within the GDA. More detailed information, regulatory documents, monitoring plans, use agreements, biological opinions, and other documents can be found at the USBR website: Monitoring results are published by the San Francisco Estuary Institute (SFEI) and are available at To ensure the quality and suitability of these monitoring efforts relative to the objectives of the GBP, this peer review was conducted to evaluate and possibly suggest ways to improve performance, and credibility of the long-term monitoring. The peer review for the GBP monitoring efforts was coordinated by SFEI and conducted by three experts in the field who were not associated with the Project. These reviewers, with expertise in environmental health science, fish and wildlife ecology, and toxicology, were Dr. Tom Grieb (TetraTech), Dr. Harry Ohlendorf (CH2M HILL), and Dr. David Janz (University of Saskatchewan). Peer review and publication are critical elements in determining the contribution and credibility of scientific findings and monitoring results. The three external experts were asked to review the monitoring program and to evaluate how well the GBP is meeting the environmental commitments outlined in the WDRs. The peer reviewers were asked to identify the GBP s strengths and weaknesses, and to suggest strategies for improving the monitoring program where feasible for the remaining duration of the GBP through To structure and guide this peer review, the following five key questions were developed:

228 226 GRASSLAND BYPASS PROJECT Is the GBP monitoring program effectively tracking the consequences (i.e., biological effects) of salt and selenium discharges to Mud Slough (north) (i.e., Stations D, I [I2], and E) and the lower San Joaquin River (Stations H [R] and N)? Is it effectively tracking potential biological effects downstream of the Merced River confluence (i.e., Station N)? 2. Is the scope and frequency of monitoring of wetland channels and critical habitat (designated habitat for listed species but critical habitat has not been designated for giant garter snake or San Joaquin kit fox) effective in tracking regulatory commitments? 3. Is the Project design based on the current understanding of the environmental science of selenium? 4. What are the key data that contribute to the better scientific understanding of the behavior of selenium in the system? How can GBP datasets be modified or improved to be more helpful to other programs (e.g., San Joaquin River Restoration Program, Bay-Delta Restoration Program, and the development of site-specific or tissue-based selenium standards by USEPA)? 5. Does the Biological Effects Monitoring Program achieve the following? If not, how can it be improved? a. Monitor selenium concentrations across all important media (water, particulates, tissue of different food web species) that contribute to selenium bioaccumulation in ecosystems. b. Identify at-risk species and their food webs to protect communities from selenium exposure. c. Determine the environmental risk occurring to fish and wildlife (including protected species such as the giant garter snake and San Joaquin kit fox) in Mud Slough (north) and lower San Joaquin River. d. Are there environmental benefits of diminished selenium in other parts of the Grasslands wetland water supply channels and the San Joaquin River? Biological monitoring in potentially improved channels has occurred at Mud Slough (north), upstream of the SLD discharge (Site C), Salt Slough (Sites F and F2), and at San Joaquin River at Fremont Ford (Site G). e. Is the GBP supporting healthy fish communities within the study area? Does the GBP monitor fish communities and abundance to be effectively integrated within other projects? f. Does the Biological Effects monitoring accomplish an assessment of the risk to human health from consumption of fish from affected channels? The review focused on the areas directly affected by the GBP and did not include other regional drainage management projects. It evaluated the comprehensive environmental monitoring program and how well it provides results for the monitored locations and parameters. The Basin Plan ( which identifies beneficial uses for the waters of the Sacramento and San Joaquin River basins, states in summary that discharges from the San Luis Drain shall not cause or contribute to pollution or nuisance and cannot be in exceedance of applicable water quality objectives resulting in degradation of beneficial uses or harm to humans, plants, animals, or aquatic life. Based on this goal, the 19 years of operation of the GBP were evaluated by the reviewers, but with a stronger focus on the recent years of the program. SUMMARY OF REVIEWS The reviewers agreed that the GBP is in compliance with the WDRs and that the scope and frequency of monitoring at the designated sampling sites are consistent with regulatory commitments. They recognized that the GBP has established a comprehensive monitoring program resulting in extensive datasets to assess changes in a variety of water quality parameters over time, but they focused their review on selenium, which was identified for the review as the primary constituent of concern for potential toxicological effects in biota downstream of the agricultural discharges. However, they agree that the toxicity as measured by laboratory bioassays is not likely related to selenium. The longterm dataset provides monitoring data of drainage-affected sites in comparison to reference sites, and the inclusion of historic data in the annual reports facilitates the understanding of temporal changes and their potential consequences to aquatic and terrestrial organisms. Additionally, seasonal changes are tracked through monthly and quarterly reporting. This is important because precipitation can influence loading of selenium and other constituents from agricultural discharges.

229 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 227 The reviewers also agreed that the sampling locations overall are appropriate to evaluate spatial trends, following a gradient approach for assessing potential biological effects, and representing the following distinct impact zones: (1) high exposure (Sites D, I2, and E), receiving direct discharge from the San Luis Drain; (2) medium exposure (Site R), ecologically relevant because of the mixing of Mud Slough and San Joaquin River water; and (3) low exposure (Site N), downstream of the Merced River confluence with the San Joaquin River, representing the effects to areas downstream of the watershed including the Delta and North San Francisco Bay. Additionally, Site I2 is also representative of an ecosystem particularly favorable for selenium bioaccumulation due to its minimal flows and lentic nature. The reviewers included several suggestions for improvements. They recommended that for reporting of results from sampling conducted under the draft 2015 Environmental Monitoring Program more emphasis be placed on describing the rationale for the monitoring effort and using the existing dataset to assess the expected performance of the continued sampling effort. Knowledge for key parameters of the magnitude and source of variability, seasonal differences, and differences among sampling locations should provide the basis for future sampling. Incorporation of information gained from previous sampling will allow refinements to the 2015 Monitoring Program in response to the lessons learned and will provide for improved understanding of the effects of the GBP. A comprehensive summary of the existing data that describes the variability, trends, cycles, and correlations in previous measurements would help with the overall goal of understanding whether the GBP has caused or contributed to pollution or nuisance conditions that exceed applicable water quality objectives, thereby resulting in degradation of beneficial uses or harm to humans, plants, animals, or aquatic life. That summary should be used to optimize future monitoring. It is extremely important that the probability for the monitoring program to yield statistically significant results is considered. With this in mind, the statistical power of the tests used in the data analyses should be determined. The power would predict the probability of correctly detecting existing trends or specified levels of differences among sampling locations. Reviewers also indicated that statistical approaches quantifying the differences between exposure sites and hydrologically and ecologically similar reference sites are a key aspect for the evaluation of biological responses. These site comparisons would allow for verification of recovery from exposure. In particular, comparing Mud Slough to a reference site (e.g., Salt Slough) could provide a dose-response relationship and a useful effects assessment if, for example, fish egg selenium concentrations would be compared to larval deformities at these sites. Adding more reference sites could provide improved understanding of the natural background levels of selenium in water and biota, which would be helpful for the GBP and other, longer-term recovery programs outside the GBP. While tissue analysis for selenium in fish, bird eggs, and invertebrates is very useful to characterize their exposure and evaluate potential effects in certain reaches within the Project area, and with that meet the requirements for the monitoring program, the biological effects monitoring could be improved. It was recommended that in addition to monitoring potential effects based on concentrations in biota, it would be beneficial to more directly evaluate biological effects as well. Additional information could be obtained by collecting eggs and sperm from spawning fish at high-exposure sites receiving selenium and similarly at reference sites. Eggs could then be fertilized and raised under controlled conditions. Selenium incorporated into yolk is used by fish larvae right after hatching, and effects are manifested as deformities or death. Dose-response relationships in the developing larvae can indicate reproductive effects through dietary exposure of the adult female fish (which transfer selenium to their eggs). With this additional test, the ecological risk assessment would be based on measurement of both exposure and actual effects. Furthermore, the conversion of whole-body selenium to egg/ovary selenium for comparison to the hazard scale developed by Lemly is outdated, and underscores the major improvement that additional fish egg collection could provide. Aqueous exposure of invertebrates and fish to selenium in the currently conducted toxicity tests does not represent the most useful information, because dietary exposure is the most important pathways for effects. Additionally, the observed toxicity may be related to any number or combination of other chemicals in the surface water samples, which can confound the test results. An improvement would be to conduct longer-term exposure testing of caged fish and invertebrates with reallocated resources, allowing evaluation of multiple dietary pathways in addition to aqueous exposure. Additionally, the selenium concentrations in fish exhibit large variation, probably because the sites are open systems with fish movement to and away from the collection sites. Caged fish testing would provide conditions that better evaluate site-specific exposures and effects.

230 228 GRASSLAND BYPASS PROJECT The fish community sampling has not shown any significant differences in community composition or occurrence of selenium-related anomalies in fish among site. This is a strong indicator of similar fish assemblages at exposure and reference sites with decreases over time in the occurrence of abnormalities in individual fish at sites receiving drainage water. If continued, the numbers of abnormalities should be standardized to the total numbers of captured fish. However, reducing the sampling sites for fish communities and dropping sites that have recovered well was recommended, and this would allow reallocation of money toward caged fish testing and fish egg collection. Another budgetary reduction could be achieved through the focus on Mud Slough as the main sampling site and reduced sampling at other sites. Sampling a greater number of sites within Mud Slough could describe transport, mixing, and deposition characteristics of selenium. Considering the reduction of biota data collection to possibly twice a year and focusing on seasons when egg development is occurring would still meet the monitoring goals for detecting spatial and temporal trends. Additionally, targeting a smaller subset of invertebrate taxa and fish species should be considered. Similar to fish eggs, eggs of reptiles, amphibians, and birds from reference and exposure sites are also the better approach for a thorough exposure assessment. Even though tadpoles have been collected and analyzed previously, they may represent a subset of amphibians that received a smaller selenium dose from their mothers and thus survived. Again, a much more sensitive approach would include the collection of eggs of amphibians and other organisms to assess the biological risk. Furthermore, the determination of trophic transfer of selenium through the food web could include measurements at the very bottom of the food web, specifically in biofilm at the sediment-water interface and suspended particulates (including phytoplankton, etc.) in the water column. This would be beneficial at sites downstream of the discharge area to better understand the assimilation of selenium and the potential dietary pathway to consumers. This information would help describe food web dynamics and could contribute significantly to creation of a conceptual model to describe overall selenium bioaccumulation. The reviewers understand that the development of a conceptual model is outside the scope of this monitoring program but the collection of biofilm and suspended particulates samples at Sites N, R, and G would better inform the ecological risk assessment for the downstream system and could additionally provide valuable data for other ecosystem-scale studies. Especially within Mud Slough, the area with the greatest impact of selenium discharges, a bioaccumulation model could help make predictions about future risks to organisms and recovery of the area. It was pointed out that waterborne selenium concentrations at Site N represent potential effects in the lower San Joaquin River, downstream of the Grassland area, well and monitoring is in accordance with requirements. Concentrations have stayed well below the 5.0 µg/l water quality objective and should not pose adverse effects to fishes. However, this objective causes some uncertainty for the ecological risk assessment since it does not consider selenium biodynamics and differences in fish feeding preferences. Selenium has complex speciation and a complex biogeochemical cycle. A better approach would be to use a tissue-based concentration from fish eggs or ovaries for Site N that can be compared to a newly developed USEPA aquatic life water quality criterion for freshwater (which is now in draft form). Alternatively, the GBP could consider lowering the water thresholds to 1.2 µg/l for lentic portions and 3.1 µg/l for lotic portions of the study area, according the USEPA draft criterion. Even though the primary emphasis of the monitoring is to demonstrate compliance with the selenium loading criterion, the reviewers recognized that many aspects of the program are highly relevant to improving the current understanding of selenium behavior in the environment, such as bioaccumulation, loading, and concentrations in abiotic and biotic components in the system. The focus on exposure and potential effects is consistent with the environmental science of selenium. However, the recommendations for more detailed ecotoxicological studies (e.g., fish and amphibian egg collection and selenium biofilm and water-column particulates concentrations) could improve the understanding of the effect of the operation of the San Luis Drain within the region and the potential effects to downstream sections of the San Joaquin River, Delta, and North San Francisco Bay.

231 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 229 Consistent improvements in water quality with regard to selenium concentrations and most other measured parameters downstream of agricultural drainwater inputs were acknowledged by all three reviewers. A significant reduction in selenium loading overall has been an important benefit to the ecology of the San Joaquin River system and associated wetlands. The San Joaquin River is a complex setting in which cumulative effects from human activities and natural occurrences upstream and downstream of the study area can make cause-and-effect assessments difficult. To provide better context on a larger landscape scale, it was suggested that selenium and other contributing stressors could be evaluated through a cumulative effects assessment. Overall, the GBP provides a unique dataset that greatly facilitates the understanding of selenium sources, transport, and bioaccumulation. The monitoring program has met the requirements of the use agreement and the WDRs. Some future modifications, mentioned above and in more detail in the individual chapters of the reviewers, could be incorporated in the draft 2015 monitoring plan to enhance the understanding of selenium behavior and the prediction of ecological risk in the San Luis Drain, the wetland channels, and San Joaquin River.

232 230 GRASSLAND BYPASS PROJECT CHAPTER 1 - REVIEW BY TOM GRIEB Introduction This review used the Grassland Bypass Project (GBP) document entitled 2015 Environmental Monitoring Program (2015 EMP; Bureau of Reclamation, 2015) as the primary description of the GBP monitoring program. In the course of the review, the requirements of the Monitoring and Reporting Program for the U.S. Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority described in the Waste Discharge Requirements (WDR; Regional Water Quality Control Board, 2015) were considered. The GBP Annual Monitoring Report (Grassland Bypass Project Oversight Committee, 2013) and the Grassland Bypass Project, EIS/EIR, Final August 2009 (2009 EIR/EIS; ENTRIX, 2009) were also reviewed to better understand the results of previous sampling and analyses. The focus of this review is on the water quality sampling and analyses. The habitat and toxicity elements of the biological monitoring are not addressed. General Observations The sampling requirements from the WDR, the sampling locations, frequency of sampling, and analytical techniques are described in adequate detail to show compliance with the WDR. However, more emphasis should be placed on describing the rationale and basis for the monitoring effort to assess environmental conditions. It is critical to the development of an effective monitoring effort to assess the expected performance of the sampling effort. This information should be developed by using existing data from the proposed sampling locations or data from comparable sites. Based on the statistical distribution characteristics of the parameters to be measured, the expected performance of the monitoring program should be described in terms of the expected magnitude and sources of variability associated with the measured parameters as well as the minimum differences between parameter values over time and/or between sampling locations that can be detected with the proposed level of sampling effort. The 2015 EMP descriptions for each section, e.g., Water Quality Monitoring, should look something like: Summary of the existing data, number of samples, summary statistics, distributional characteristics of key parameters, indication of seasonal effects, differences between sample locations. Most of this information is available elsewhere, e.g., in the 2009 EIS/EIR. A summary of the relevant information from that report would make the 2015 EMP more complete and should be used to provide the basis for the sampling design. Synthesis of the existing data and a statement of how the data characteristics influenced the design of the monitoring program. Description of the sampling design. The sampling elements, station locations, parameters, sampling frequency are described in the 2015 EMP. Description of the expected sampling results and how the data will be analyzed and used. Here are some specific comments and questions about the 2015 EMP Report that was reviewed: P. 12, 5: The GBP 2015 Environmental Monitoring Program includes water quality parameters plus several other sites to assess the restoration of the area with the removal of agricultural drainwater under the GBP. It s not clear if these assessments of the restoration efforts will be conducted as part of the 2015 EMP or as part of other programs. In either case, how these assessments will be conducted and what is expected to be achieved is of interest to a better understanding of the GBP s environmental effects and should be described in detail. P. 14, Section 3.2 Integration with Research/Investigations Activities. Here is the opportunity to describe relevant research activities and how the data will be used to advance the understanding of the effect of the GBP. The collection of additional measurements without a plan for using the data in this program (or in collaboration with other ongoing efforts) could result in a missed opportunity. P. 18 2: Reclamation will incorporate data collected for other programs in the GBP monthly and quarterly reports. Identify these other programs. Describe these data, and how the information will be used. P. 19, San Luis Drain. The concentration of selenium in sediment will be measured in the ten places. Why 10 locations? How will the data be used? It seems that a plan for the collection of sediment data, TSS, flow, water column Se concentrations could be used to characterize the transport and behavior of Se in the drain system.

233 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 231 P. 19, Mud Slough (north). Has Site C been dropped because it will be monitored by other programs? How will the monitoring results in Mud Slough be used to assess the effects of the GBP without information from the upstream station? Will the data from the Westside Coalition be comparable? P. 20, San Joaquin River. The GBP 2015 Environmental Monitoring Program will continue to evaluate the impacts of the GBP on the San Joaquin River at three places: What has been learned from the previous sampling, and how has this information been incorporated into the 2015 EMP? How will these data be used to assess flows and contaminant concentrations in water? Is the goal to determine the effects of the GBP at specific distances? What are the mixing characteristics of the GBP discharge? P. 20 Stormwater Monitoring. The description of the stormwater monitoring is incomplete. Yet this seems like a great opportunity to describe the effects of large, episodic discharges. Are there some critical factors that should be measured? Critical timing? Critical locations? P Reduce the frequency of sampling nutrients Why? What s the rationale? P. 21, Section 6.0 Flow Monitoring. Flow in the San Luis Drain must be managed to prevent erosion of sediments. What data support this, what are the critical flow characteristics? P. 22, 6.6 Load Calculations. How are the load estimates from these calculations influenced by the sampling frequencies for Se? Here is a specific example to show the existing data, describe what has been learned from previous sampling efforts, and to explain how the 2015 EMP has been developed in response to this information. It appears that the data will be collected by several entities (multiple agency responsibility), and reported or saved in different databases, e.g., the flow data stored in USGS database. All data from the GBP should be made readily available/accessible. P. 24, Section 7.0 Water Quality Monitoring. The historic data have been used to develop regulatory programs for the control of agricultural drainage discharges. What have these data shown, and how have these results been utilized in the design of this program? What are the critical data issues (e.g., the importance of a continuous record to characterize data distributions and the ability to define statistical ranges on parameters)? P. 27, 7.3 Water Quality Parameters:»» What has been the performance of the monitoring efforts to date?»» Nutrients: why these parameters and sampling frequencies? What have we learned and what do we expect to get out of the program moving forward?»» Mercury in water will also be measured at four places that convey GBP water. Why 4 places? What s been observed in the past? In general, there isn t much data available to characterize mercury or methyl mercury loads from irrigated agriculture in California. There may be an opportunity to contribute to this understanding but the level of sampling would have to be increased, other parameters such as DOC, EC, TSS, total and MeHg would have to be measured simultaneously, and the sampling strategy would have to be thought through. It s not at all clear what the contribution of these measurements at four places will be. Responses to Key Questions 1. Is the GBP monitoring program effectively tracking the consequences (i.e., biological effects) of salt and sele nium discharges to Mud Slough (north) (i.e., Stations D, I [I2], and E) and the lower San Joaquin River (Station H [R] and N)? Is it effectively tracking potential biological effects downstream of the Merced River confluence (i.e., Station N)? Considering the sampling of the water quality parameters, e.g., elevated salt, selenium and mercury, there appears to be several opportunities for examining the link with biological effects downstream. But it is not clear that the existing sampling effort will take full advantage of these opportunities. Items to consider:»» It is not clear what sampling will be conducted at Site C (that will be monitored by the Westside Coalition for the Irrigated Lands Regulatory Program). Coordinated sampling should be conducted at locations both upstream and downstream of the discharge to better understand the magnitude and a real extent of discharge effects. (Note: After these comments were submitted, the revised 2015 Environmental Monitoring Plan includes sampling at Site C again.)

234 232 GRASSLAND BYPASS PROJECT »» Station D is located about a quarter mile below the SLD discharge (2015 EMP, p. 27). This distance from the discharge is most likely not adequate to characterize local effects and the areal extent of effects of the discharge. Sampling a greater number of locations near the discharge could be conducted to describe the mixing of the discharge in Mud Slough and the attenuation of effects with distance. Linking the water column sampling to sediment sampling could also be done to characterize the mixing of the discharge and the deposition of suspended material. 2. Is the scope and frequency of monitoring of wetland channels and critical habitat (designated habitat for listed species but critical habitat has not been designated for giant garter snake or San Joaquin kit fox) effective in tracking regulatory commitments? Not addressed by this reviewer. 3. Is the project design based on the current understanding of the environmental science of selenium? The primary emphasis of the monitoring program is on demonstrating compliance with the selenium loading criterion. The primary ecological concern of selenium is the bioaccumulation of selenium and the effects on wildlife. A key to understanding the potential effects on wildlife is the ability to understand the form of selenium, the level of exposure to prey items, and the bioaccumulation in the food web. A large effort has been made by the USGS in the development of ecosystem-scale selenium modeling in support of fish and wildlife criteria development (Presser and Luoma a,b). Their work has shown that one of the keys to understanding selenium bioaccumulation is to characterize the form of selenium exposure to organisms. In the 2015 EMP there is little emphasis on expanding the current understanding of the form of selenium discharged or the transformations that take place that might affect bioaccumulation potential. The measurement of dissolved selenium and selenium in suspended particulates is limited to quarterly samples. The efficacy of quarterly sampling to characterize the importance of dissolved and particulate forms of selenium on potential biological effects is not addressed in the 2015 EMP. Understanding dissolved and particulate material selenium speciation is extremely important in assessing the assimilation efficiency of Se by prey items. However, speciation is not part of the monitoring program. 4. What are the key data that contribute to the better scientific understanding of the behavior of selenium in the system? How can GBP datasets be modified or improved to be more helpful to other programs (e.g., San Joaquin River Restoration Program, Bay-Delta Restoration Program, and the development of site-specific or tissue-based selenium standards by US EPA)? An important issue associated with the July 2015 Draft Bay Delta Conservation Plan/California WaterFix EIR/EIS is the effect of an increase in the relative proportion of San Joaquin River flow compared to Sacramento River flow on selenium concentrations in North San Francisco Bay (listed on the (d) list for selenium impairment). The modeling analysis in the 2015 EIR/EIS shows, for example, that there is an increase in the load to North San Francisco Bay from the existing conditions by 6 11 %, e.g., for the different alternatives considered as part of Alternative 4. It is of interest of how the data from the 2015 EMP can be used to quantify the effect of the operation of the SLD on selenium concentrations on the San Joaquin River at Vernalis and the potential contribution of selenium loading to North San Francisco Bay. 5. Does the Biological Effects Monitoring Program achieve the following? If not, how can it be improved? a. Monitor selenium concentrations across all important media (water, particulates, tissue of different food web species) that contribute to selenium bioaccumulation in ecosystems. As noted above, the infrequent sampling of particulate and dissolved Se and the lack of Se speciation limit the use of the expected data in assessing the contribution to Se bioaccumulation. However, fully meeting that objective would require a greatly expanded sampling effort. It is important to meet fewer monitoring objectives successfully than to unsuccessfully address multiple objectives. b. Identify at-risk species and their food webs to protect communities from selenium exposure. Not addressed by this reviewer

235 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 233 c. Determine the environmental risk occurring to fish and wildlife (including protected species such as the giant garter snake and San Joaquin kit fox) in Mud Slough (north) and lower San Joaquin River. Not addressed by this reviewer d. Are there environmental benefits of diminished selenium in other parts of the Grasslands wetland water supply channels and the San Joaquin River? Biological monitoring in potentially improved channels has occurred at Mud Slough (north), upstream of the SLD discharge (Site C), Salt Slough (Site F and F2), and at San Joaquin River at Fremont Ford (Site G). Not addressed by this reviewer e. Is the GBP supporting healthy fish communities within the study area? Does the GBP monitor fish commu nities and abundance to be effectively integrated within other projects? Not addressed by this reviewer f. Does the Biological Effects monitoring accomplish an assessment of the risk to human health from con sumption of fish from affected channels? Not addressed by this reviewer Conclusions and Recommendations The 2015 Environmental Monitoring Program demonstrates compliance with sampling requirements from the WDR. The sampling locations, frequency of sampling, and analytical techniques are described in adequate detail. However, more detailed information on the nature of existing conditions and the projected effectiveness of the 2015 EMP is needed if a goal is to show how the program will contribute to the understanding of the environmental conditions in the San Luis Drain and the receiving water (Mud Slough). The demonstration of how the program will contribute to the understanding of the environmental system can be developed by describing existing conditions and presenting how the results of the monitoring program will enhance the existing knowledge. References Bureau of Reclamation, Grassland Bypass Project 2015 Environmental Monitoring Program. September 1, 2015 December 31, Revised: 14 August ENTRIX, Grassland Bypass Project, EIS/EIR, Final August State Clearinghouse No Grassland Bypass Project Oversight Committee, Grassland Bypass Annual Monitoring Report Contribution No San Francisco Estuary Institute. Richmond, CA. Presser, T.S. and S.N Luoma. 2010a. Ecosystem-Scale Selenium Modeling in Support of Fish and Wildlife Criteria Development for the San Francisco Bay-Delta Estuary, California. Administrative Report, December Presser, T.S. and S.N Luoma. 2010b. A Methodology for Ecosystem-Scale Modeling of Selenium. Integrated Environmental Assessment and Management 6(4): Regional Water Quality Control Board, Attachment B to Order R Waste Discharge Requirements. Monitoring and Reporting Program for the U.S. Bureau of Reclamation and the San Luis & Delta-Mendota Water Authority described in the (WDR)

236 234 GRASSLAND BYPASS PROJECT CHAPTER 2 - REVIEW BY DAVID JANZ Introduction The Grasslands Bypass Project (GBP) began in 1996 with the goal of diverting unusable sub-surface agricultural drain water from the approximately 97,000 acre Grasslands Drainage Area (GDA) to avoid potential ecological impacts to biota inhabiting surrounding grasslands habitats. These habitats include (1) wetlands utilized by waterbirds and certain other wildlife (mammals, reptiles and amphibians) that are susceptible because they prey upon aquatic organisms, and (2) the San Joaquin River and its tributaries utilized by fishes for feeding, migration, and reproduction. A major impetus for development of this project was observations in the early 1980s of early life stage developmental toxicities (deformities) and mortality of aquatic birds feeding in the Kesterson Reservoir, part of the Kesterson National Wildlife Refuge, which received agricultural drain water from areas similar to the GDA. Although the drain water contained elevated levels of several trace elements, including selenium, boron, molybdenum, arsenic and chromium, and associated ions, selenium was identified as the causal agent responsible for these effects in birds. At that time, scientific investigations into the aquatic ecotoxicology of selenium were first being reported, and the ecoepidemiological work at Kesterson Reservoir represents one of the classic case studies on this topic (Skorupa 1998; Ohlendorf 2002; Young et al. 2010). Other than mercury, selenium contamination of aquatic ecosystems represents the greatest ecotoxicological hazard of all trace elements to biota that feed in such systems (Luoma and Presser 2009). This is especially true for oviparous (yolk-bearing) vertebrate animals: fishes, birds, amphibians and reptiles (Janz et al. 2010). During oogenesis in oviparous vertebrates, synthesis and transport of yolk to eggs (i.e., vitellogenesis) by reproductively mature females results in excess selenium obtained by females via their diet to be maternally transferred to eggs in an unregulated, dose-dependent manner. When yolk and albumin are utilized by embryos and/or hatched offspring as an energy source during these sensitive early life stages, excess selenium is biotransformed to reactive metabolites that are believed to cause toxicity (Spallholz 1994; Janz et al. 2010). These early life stage toxicities are characteristic and diagnostic of elevated selenium exposure, and include skeletal, craniofacial, limb and eye deformities, edema, and mortality. Such toxic effects have been shown to have significant negative impacts on fish populations by reducing recruitment of new individuals into populations, and provide one of the clearest cause-effect relationships in ecotoxicology between exposure to a toxic substance and impaired population dynamics (Lemly 1993; Skorupa 1998; Janz et al. 2010). Although selenium is an essential trace micronutrient, there is a very narrow range between essentiality and toxicity, particularly in oviparous vertebrates, which further exemplifies the hazard posed by this trace element to susceptible aquatic-dependent vertebrates. From a regulatory perspective, there has been much debate in recent years concerning revisions of water quality criteria (WQC) for selenium aimed at protecting aquatic biota. The present United States Environmental Protection Agency chronic WQC of 5 µg Se/L causes great uncertainty in the ecological risk assessment of selenium. This is because differences in feeding preferences, geochemistry, hydrology and ecology among aquatic ecosystems dictate the speciation, bioavailability and toxicity of Se to aquatic vertebrates (Luoma and Presser 2009; Stewart et al. 2010; Janz 2012). In other words, an ecosystem with 1 µg Se/L in the water column can potentially pose a greater risk to aquatic-dependent species than an ecosystem with 10 µg Se/L. There is now consensus among scientists and regulators that (1) dietary exposure is the dominant route of uptake in aquatic vertebrates, (2) fishes are the most sensitive vertebrate class to selenium toxicity, (3) measurement of selenium in eggs of oviparous vertebrates, particularly fishes, provides the most accurate assessment of ecological risk, and (4) there often needs to be some form of site-specific assessment of selenium biodynamics in selenium-contaminated aquatic ecosystems. Thus, the current draft USEPA aquatic life ambient water quality criterion for freshwater is tissue-based, with selenium concentration in fish eggs or ovary proposed as the most accurate means to assess ecological risk to all aquatic biota. Selenium is an insidious aquatic contaminant due to its persistence in abiotic and biotic compartments of freshwater ecosystems; indeed it behaves more like notorious persistent organic pollutants such as organochlorine compounds. Selenium has one of the most complex patterns of speciation among trace elements, and biogeochemical cycling of these different chemical forms in aquatic systems is equally complex (Maher et al. 2010; Janz et al. 2014). Combined with the fact it is an essential trace element actively taken up by organisms, it is unknown how long selenium will persist in the food web of a given contaminated ecosystem even after loading has ceased. Thus, monitoring programs that assess the recovery of aquatic systems historically receiving large selenium loading must be conducted over the long term (years to decades).

237 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 235 Due to the above rationale, and given my expertise in the aquatic ecotoxicology of selenium, the focus of my comments will be on selenium. When appropriate, I will offer comments on other constituents (e.g., other trace elements, ions, pesticides) but these comments will be brief and hopefully other invited contributors will expand on these aspects of the GBP monitoring program. It is my belief that selenium loading from the GDA represents the primary ecotoxicological concern in the San Joaquin River and associated wetlands, and if selenium is maintained at levels in biota that do not pose ecotoxicological risks, then other constituents will likely follow suit and also not pose such risks. General Observations The GBP has recently completed its 19th year of operation, and to date there have been consistent improvements in water quality associated with loading of selenium and most other measured constituents at monitoring stations downstream of agricultural drain water inputs. This is particularly true for the past 3-4 years, although this may be confounded by the relative lack of annual precipitation over this period. By 2014, selenium loading from the GDA has been reduced to less than 5% of the pre-project ( ) average. Overall, based on data available from the comprehensive GBP monitoring program it appears that achieving the water quality objective (WQO) of 5 µg Se/L by 2019 is achievable in all downstream environments with the possible exception of within Mud Slough. However, regulations change as science progresses, and therefore the GBP should anticipate a lowering of this WQO prior to the end of this project; refer to the draft USEPA criterion based on aqueous selenium concentration (1.2 µg Se/L for lentic systems and 3.1 µg Se/L for lotic systems, monthly average). Of note, and I imagine some concern, is the fairly consistent increase in invertebrate and fish selenium concentrations that occurred in 2014 in Mud Slough (sites D and I2). Responses to Key Questions 1. Is the GBP monitoring program effectively tracking the consequences (i.e., biological effects) of salt and selenium discharges to Mud Slough (north) (i.e., Stations D, I [I2], and E) and the lower San Joaquin River (Station H [R] and N)? Is it effectively tracking potential biological effects downstream of the Merced River confluence (i.e., Station N)? General comments The GBP has established a comprehensive monitoring program to assess temporal changes in a variety of water quality parameters and potential toxicological effects in biota at several locations downgradient of agricultural drain water inputs. This long-term dataset provides useful information to assess changes in water quality and biological effects over almost two decades on an annual basis, but also importantly changes that occur within years on a seasonal basis. This is important because of distinct seasonal differences in precipitation in this area, which can influence loading of selenium, salts, and other constituents of agricultural drain water. In general, the GBP monitoring program is effectively tracking water quality parameters in both time and space, but is lacking somewhat on biological effects monitoring, as will be discussed below. In addition, certain aspects of the monitoring program are not essential, and these resources could potentially be directed more towards focused studies on biological effects associated with selenium exposure in vertebrate animals.

238 236 GRASSLAND BYPASS PROJECT Selection of monitoring sites The monitoring sites listed above are appropriate locations to collect samples, as they fall into three distinct impact zones: (1) within Mud Slough (sites D, I2 and E), which currently receives the majority of constituents from the GDA and can be considered a high exposure area, particularly the furthest downstream site (E), (2) site R, perhaps the most ecologically relevant monitoring station since it is upstream of the Merced River confluence on the San Joaquin River and represents the full influence of the GBP loading after mixing with the San Joaquin River (medium exposure area), and (3) Site N, located on the San Joaquin River downstream of the Merced River confluence (low exposure area). These sites follow a classic gradient approach for assessing potential biological effects of aquatic pollution (Fox 1991). As discussed below, Mud Slough represents a key monitoring area for future investigations since it appears to be the zone of most influence as the GBP has evolved to minimize GDA inputs arising from wetland water supply channels to areas such as Salt Slough. Site I2, a periodically flooded backwater of Mud Slough, is an important monitoring site since it provides an ideal environment for selenium assimilation into the food web due to its lentic nature and potentially important habitat for fish reproduction. Site G, located on the San Joaquin River upstream of the Mud Slough confluence at Fremont Ford, now represents an appropriate reference site for sessile organisms (e.g., invertebrates and perhaps fishes with very small home ranges), but not fishes that migrate to any extent since it will be unknown whether they have spent time in downgradient exposure areas, including Mud Slough. It is surprising that the 2015 monitoring program was modified to exclude site G. Without an appropriate reference site to compare data collected from exposure sites, it is unclear how recovery of the exposure sites can be verified statistically. It is recommended that site G be retained as a reference site, and it is also suggested that an appropriate reference site located further (>10 miles) upstream of site G be incorporated into the monitoring program to avoid potential issues with migrating organisms, particularly small-bodied ( bait ) fishes. If such a site is chosen, it will be important to select a location that is hydrologically and ecologically similar to sites G, R and N. This raises a key point about the importance of appropriate reference sites in monitoring programs. The GBP monitoring program has many exposure sites, but relatively few reference sites, in fact none that I am aware of located upstream of all GDA inputs or in an ecologically and hydrologically similar area outside the immediate vicinity. It is recommended that the GBP include an additional reference site(s) outside the immediate zone of GDA influence to provide further comparison of the many parameters being determined. This may be especially important over the next 5 years as the GBP comes to an end. It is also important because it is not apparent that the current monitoring program addresses the issue of natural background levels of selenium in water or biota in this region. In my opinion this approach would also be useful for longer term recovery initiatives such as the San Joaquin River Water Quality Improvement Project (SJRIP). (Note: After these comments were submitted, the revised 2015 Environmental Monitoring Plan includes sampling at Site G again.) Based on the rationale provided in the preceding paragraph, my discussion will focus on monitoring of the core area : Mud Slough and the sites immediately above (G) and below (H, R) its confluence with the San Joaquin River. I have reviewed the long term data available from monitoring Salt Slough, and it is evident that diversions of agricultural drain water from this waterbody have successfully reduced selenium loading to the San Joaquin River, leaving Mud Slough as the area of most concern with respect to the 2019 end-date of the GBP. There are also data I have reviewed from other sampling sites, some of which have included bird eggs and tadpoles, but for the sake of brevity I will focus on the aforementioned monitoring sites. Many of the comments I will provide are applicable to other monitoring sites beyond the core area mentioned above. Cumulative effects assessment It is important to note here that the San Joaquin River represents a confounded system where cumulative effects are present from human activities, and natural phenomena, occurring upstream throughout the watershed. It may be worth thinking to some extent about the GBP in terms of larger scale cumulative effects assessment (CEA) in order to provide more context into the relative contributions of other stressors to the San Joaquin River, both upstream and downstream of the study area. Cumulative effects assessment uses an effects-driven approach to assess environmental impacts on multiple landscape scales. Several recent publications are available to provide guidance on CEA, including an entire issue of the journal Integrated Environmental Assessment and Management devoted to this issue (volume 9(3), 2013). Although it is realized that the GBP monitoring program is focused primarily, and correctly, on potential biological effects of the GDA on immediate, smaller scale receiving environments, it may be worthwhile to include discussion of larger scale aspects in future reports. This may include referring to the recently completed Total Maximum Daily Load for Selenium in the North San Francisco Bay report. This will provide a context for the role of the GDA within the entire San Joaquin River watershed.

239 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 237 Specific comments THE IMPORTANCE OF EGG SELENIUM DETERMINATIONS Since the GBP monitoring program has evolved to some extent since its inception, I will be referring mainly to the most recent documents available, provided to me as the draft report (zipped file), the document dated August 14, 2015 titled GBP 2015 Environmental Monitoring Program, and the some extent the most recently available GBP Annual Report ( ). From 2012 to 2014 (and presumably 2015, but data may not yet be available), the California Department of Fish and Wildlife (CDFW) has conducted sampling of fishes, invertebrates, bulrush (Typha) seed heads, and plankton from sites E, G, and H on a quarterly basis. Site R replaced site H in July 2013 to avoid possible dilution issues associated with the Merced River; I completely agree with this change to the monitoring program as mentioned above. Samples were analyzed for total selenium (using hydride generation AAS) and boron (using ICP-MS). It was unclear from the information provided whether plankton included zooplankton and/or phytoplankton, and I did not see any selenium data in the most recent draft report (I am assuming based on the description of methods by CDFW, that this is zooplankton). It is suggested that this be specified. The CDFW monitoring has also included a fish community assessment at sites G, E, and H (replaced by R in 2013) since before implementation of the GBP monitoring program (1993). Overall, this is a robust monitoring program aimed at assessing exposure to selenium and boron, but has limited value in assessing the effects of exposure to drain water from the GDA. Potential effects assessment ideas will be brought forth later in this section. As mentioned previously, it is now agreed by scientists and regulators that measurement of selenium in eggs or ovary of fishes provides the most important (accurate) data to inform ecological risk assessment. Although the GBP includes collection of bird eggs in the Grasslands area for selenium analysis and observations of mortality of embryo malformations, a major gap is the lack of fish egg collections. Thus, one of my major recommendations is that the GBP monitoring program include collection of resident fishes during the prespawning or spawning period in order to obtain eggs for selenium analysis. Importantly, for many fishes this can be achieved nonlethally, allowing release of fish after sampling. In small-bodied fishes, it will be necessary to obtain composite samples from 5-10 fish to obtain sufficient egg mass for selenium analysis, but for larger-bodied fishes there will likely be sufficient mass from a single individual. (It is worth noting here that switching the selenium analyses from HG-AAS to ICP-MS will likely reduce the mass of sample required to reliably quantify total selenium, although it is realized that there is rationale for using the same laboratory for the remainder of the GBP for consistency). In many cases eggs can be expressed manually from fishes by gentle pressure on the abdomen. If this does not work, mature female (and male) fish can be induced to ovulate by injection of gonadotropin-releasing hormone (GnRH) analogues such as Ovaprim, left in net pens overnight, and then sampled the following day. Egg collection can also be conducted lethally by dissecting out eggs/ ovary after euthanasia. The life history of each fish species will need to be consulted to know when spawning occurs. It is important to note that there are two main patterns of oogenesis in fishes: (1) synchronous spawners, where all eggs are at the same developmental stage during maturation and spawning occurs in a single (or in some species several closely-timed) event (e.g., salmonids, suckers), and (2) asynchronous spawners, where eggs are at different stages of oogenesis and repeat spawning occurs over an extended period of weeks to months (e.g., cyprinids such as minnows). Asynchronously spawning fish species provide better logistics since the timing of fish sampling, and thus availability of mature eggs, occurs over a greater window of time. The current monitoring timelines for quarterly biological sampling may need to be more flexible to match the timing of fish spawning. Chinook salmon and steelhead trout are iconic fish species and important ecological and cultural components of the San Joaquin River, especially given the recent re-introduction of chinook into the river and long-term goals of enhancing both species presence. Both of these salmonid species are synchronous spawners and eggs are easily collected nonlethally during the spawning period. If any opportunities arise to collaborate with fisheries biologists or hatchery staff in order to obtain eggs from either species, it is suggested that these samples be collected for selenium analysis.

240 238 GRASSLAND BYPASS PROJECT Similar to fishes, collection of amphibian, reptile or bird eggs from exposure and reference areas are the ultimate samples to obtain for selenium exposure assessment. Frog egg masses are collected during the breeding period, and only a fraction of the egg mass is usually required for selenium analysis. Although tadpoles have been collected sporadically during the GBP monitoring program for selenium analysis, frog eggs are a better option. This is because there will be significant growth dilution of selenium in tadpoles compared to eggs, and also potentially that tadpoles may represent the survivors that received lower selenium doses from their mothers compared to embryos with greater selenium doses that perished prior to the tadpole stage. Waterbirds usually build nests on the ground near waterbodies, particularly on islands or other refuges, and for many bird species if a single egg is removed from the nest the female will replace it. This is definitely true for ospreys as well. It appears the GBP monitoring will include bird egg collections from the Grasslands area. Reptile eggs, notably those laid by the giant garter snake, will be hard to come by and given this species conservation status it is not likely permits will be issued for collection. Since Mud Slough appears to be the area of most concern with respect to the long term goals of the GBP, it is recommended that a more intensive monitoring program be conducted at this high exposure area for the duration of the project, focusing on collection of eggs from fishes, amphibians, birds, and potentially reptiles. In the absence of egg selenium data, whole-body or muscle selenium concentrations provide the next best information for risk assessment. The current GBP monitoring program is effectively tracking such tissue selenium concentrations in a variety of fish species, and occasionally amphibians (tadpoles) at sites outside the core area. The reason for uncertainty in using whole-body or muscle selenium for risk assessment is that there is significant variability among species in relationships to egg/ovary selenium concentrations. However, in the absence of egg/ovary selenium data then the current monitoring of whole-body selenium in smaller fishes and muscle selenium in larger fishes is an effective approach. It should be noted that muscle samples can be collected nonlethally from large-bodied fishes through the use of muscle plugs, which provide sufficient mass for selenium analysis. CAGED FISH AS BIOMONITORS Another monitoring approach that might be considered is the use of caged small-bodied fish for assessing exposure to selenium and other constituents of the GDA discharges. This approach has been used successfully for exposure assessment in many scenarios where more controlled conditions are needed, especially with respect to fish mobility (Palace et al. 2005; Allert et al. 2006; Oikari et al. 2006; Phibbs et al. 2011a,b). Fish migration in and out of exposure areas, such as Mud Slough, may be responsible for the large variation observed in tissue selenium concentrations of fishes collected at this and other GBP monitoring sites. In caging studies, relatively small sinking cages (0.5 m3) are deployed with fishes (commonly minnows) in each cage. Fish are able to feed on available benthic and pelagic invertebrates, and graze on periphyton/biofilm, depending on their feeding niche. For selenium bioaccumulation, it has been established that days are required for fishes to reach steady state equilibrium with respect to selenium bioaccumulation (Allert et al. 2006; Phibbs et al 2011a). Detailed guidance for conducting such caging studies is available (Palace et al. 2005). For the GBP monitoring program, fathead minnow would be an ideal fish species to use, since it is readily available commercially, is resident in the area (although introduced), has a short life cycle, is omnivorous, and is an asynchronous spawner. It is highly recommended to use fathead minnow caged for 60 days at sites G (reference), N, R and E (or D or I2) to assess bioaccumulation of selenium in eggs. It may also be a consideration to cage minnows at site F or F2 in Salt Slough, since these sites have recovered significantly in the past decade with respect to selenium inputs, and they are likely more ecologically and hydrologically similar to Mud Slough, thus a valid reference site. It should also be noted that simple approaches are also available to use caged benthic invertebrates at study sites (Franz et al. 2013). As discussed below, these approaches are far superior to standardized laboratory toxicity tests for selenium and other constituents of the GDA discharge into Mud Slough. THE IMPORTANCE OF PRIMARY PRODUCERS Another major recommendation is to include a more comprehensive determination of selenium concentration at the base of the food web at sites G, N, R and E. At these sites, assimilation of dissolved inorganic selenium by the biofilm/periphyton (hereafter referred to as biofilm) layer at the sediment-water interface will be a critical process dictating further trophic transfer through the food web, although algae in the water column may also be important (Fan et al. 2002; Stewart et al. 2010; Janz et al. 2014). It appears that there will be monitoring of dissolved and particulate selenium, but I could find no details on this approach. It is assumed that water samples will be filtered to distinguish between dissolved selenium and selenium bound to particulate matter. However I could find no data on dissolved vs. particulate selenium; perhaps this is a new aspect of the GBP monitoring program initiated in Regardless, selenium incorporated into biofilm will represent a key step in the assimilation of selenium into the food web and should be considered as an addition to the monitoring program.

241 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 239 Biofilm is a complex matrix composed of algae, bacteria and fungi as the primary biotic components. Many organisms within biofilm are able to actively take up inorganic selenium and convert it to more toxic organoselenium species that are then trophically transferred through dietary pathways to consumers (i.e., benthic invertebrates, fishes, birds, and other vertebrates). Although trophic transfer of organoselenium via diet is relatively consistent among food webs, assimilation or enrichment by biofilm is highly variable due to a number of abiotic and biotic factors. The GBP monitoring program already has important selenium data from consumers in food webs. Including selenium analyses of biofilm at different sites will allow creation of conceptual models at each site that better describe the overall selenium bioaccumulation. This is the only major data gap I see in the GBP monitoring program, other than the lack of fish egg selenium data. Thus, it is highly recommended that the GBP monitoring program include selenium determinations in biofilm. Biofilm is easily collected by scraping rocks along shorelines and/or deploying tiles into waterbodies to allow colonization (the latter technique is likely preferable). Although the GBP includes sediment monitoring for selenium concentration, it is the top 5-10 mm layer of sediment (the biofilm layer) that is the critical component, since this is where all the action occurs with respect to selenium assimilation and incorporation into food webs. As stated above, this site-specific information on food web dynamics will better inform the ecological risk assessment of selenium in these systems. A further step would be to develop a biodynamic model of selenium behavior at tmud Slough (Presser and Luoma 2010), which is discussed later in this chapter. FISH COMMUNITY SAMPLING Unlike human health risk assessment, which is focused on the toxicological risk to individual humans, the goal of ecological risk assessment is to protect populations and communities of non-human organisms. In other words, the ultimate question is whether anthropogenic activities threaten the sustainability of individual species at impacted sites. Fish (and invertebrate) community assessments are thus important approaches to address this question. Monitoring of fish communities has been conducted since 1993 at several sites, with no clear differences over time or among sites; this may be due to lack of statistical power to detect biologically significant differences. In addition, fish mobility likely plays a role since these monitoring sites represent an open system where fish are free to move among sites. Another problem with traditional fish community assessments is that they often involve lethal sampling of fishes, usually by gillnetting. I could not find details about the methodology, but if this is the case it raises the question of whether the fish community monitoring causes a greater impact on community structure than the constituents within drainage water that are of concern. Alternatively, if beach seining or other nonlethal techniques were used to sample fish communities then this should have a relatively minor impact. Overall, this long-term fish community assessment is a strong aspect of the monitoring program, indicating that somewhat similar fish assemblages are present at sites representing a gradient of selenium exposure. It also appears that the CDFW has examined each fish captured during the community assessments and provided data on observed anomalies, which appear to be decreasing over the past 6-8 years (GBP Annual Report, chapter 7, Figs 14-16). I was not able to evaluate these Figures since the y-axis is not labeled, and it appears that these are the actual number of observations without standardizing to the total number of fish captured (i.e., frequency or percentage). LABORATORY TOXICITY TESTING It is well established that aqueous exposure of invertebrates and fishes to selenium is not a relevant exposure pathway in aquatic ecosystems, since toxicity occurs at dissolved selenium levels orders of magnitude greater than during dietary exposure. Thus, the quarterly chronic three-species toxicity testing currently in place is irrelevant to selenium exposures that would occur at any of the sites. However, other constituents entering exposure sites from the GDA (e.g., boron) may cause toxicity in laboratory tests, so this may be the rationale for continuing these tests. It is suggested that the current laboratory toxicity testing be re-evaluated, since these resources could be allocated to other, more relevant activities. An example would be the use of caged fish and invertebrates mentioned previously, since this would allow for exposures from multiple dietary pathways, in addition to aqueous exposure to other constituents of the GDA discharge. EFFECTS ASSESSMENT As mentioned previously, the GBP has established a comprehensive long-term monitoring program that effectively assesses exposure of biota to selenium and boron. This is summarized for selenium nicely in Table 4a of the GBP annual report, which shows changes in the selenium hazard scale developed by Dennis Lemly. This Table shows clearly that the aquatic hazard to fishes has decreased dramatically over the first 15 years of the GBP. However there is significant uncertainty in Table 4a because a generic formula from 20 years ago was used for converting whole-body selenium to egg/ovary selenium. This further illustrates the need to collect fish eggs during future monitoring activities.

242 240 GRASSLAND BYPASS PROJECT Ecological risk assessment is based on both exposure and effects assessment. Unfortunately the GBP monitoring program has collected relatively little effects-based data. In my review of the significant amount of information available, I did not see even basic morphometric data (body length, body weight, Fulton s condition factor) for collected fish. Perhaps these data are available but I could not find them. As stated previously, the observed anomalies reported in chapter 7 of the annual report are meaningless without some standardization to the total number of fish captures. The ideal approach to conduct an effects assessment for selenium is to collect gametes (eggs and sperm) from spawning fish inhabiting exposure and reference areas, fertilize the eggs in the laboratory or in the field, and raise the embryos to the swim-up (fry) stage under controlled conditions in a laboratory. Selenium incorporated into yolk proteins during vitellogenesis is utilized by larval fish following hatch and just prior to swim-up, and this is when the fish receive their ultimate dose of maternally-transferred selenium, and when characteristic deformities manifest. The frequency of total deformities in fry is plotted as a function of egg selenium concentration (determined in a different subset of eggs from the same adult female) across all sites to describe a dose-response relationship. This is the approach used for several of the data points in the species sensitivity distribution (SSD) used by the USEPA in their derivation of the draft water quality criterion for selenium in freshwater. It is realized that this field-based effects assessment may be beyond the scope of the GBP monitoring program, but nonetheless it is worth mentioning here since it provides both exposure and effects assessment from fish exposed chronically to dietary selenium in situ. 2. Is the scope and frequency of monitoring of wetland channels and critical habitat (designated habitat for listed species but critical habitat has not been designated for giant garter snake or San Joaquin kit fox) effective in tracking regulatory commitments? I am not familiar with regulations in California associated with definitions of critical habitat, but can offer the following comments. The ongoing fish community assessments provide detailed lists of species captured, their abundances at monitoring sites, and their current conservation status. As mentioned previously, the GBP monitoring program is comprehensive in terms of the number of exposure sites, frequency of sampling, and the variety of parameters being assessed. At this point in time, it appears that Mud Slough is the area of greatest concern with respect to selenium and other constituents discharged from the GDA. The aquatic habitats and surrounding terrestrial habitats are thus of greatest concern with respect to providing a healthy environment for fish and wildlife to meet their ecological requirements. If resources need to be reallocated, I suggest that a more focused monitoring program be conducted in and around Mud Slough for the duration of the GBP, with perhaps less resources allocated towards other exposure sites that have recovered substantially in the past decade. It may also be worth developing a site-specific model for selenium bioaccumulation in Mud Slough that can provide future predictions of an aqueous selenium concentration that will protect aquatic life. With respect to the giant garter snake, previous attempts at sampling this rare species have been fruitless. In my opinion Mud Slough and surrounding terrestrial habitat represent the greatest, and perhaps only, toxicological risk associated with GDA discharges to this reptile in the study area, and should be the focus of remediation efforts to provide critical habitat. However there are many other factors other than selenium, boron and salts that are likely more important, such as adequate prey, breeding sites, cover, etc., that are not necessarily impacted by toxic agents. As far as the kit fox, mammals are far less sensitive to selenium exposure than oviparous vertebrates. Although this species may forage on aquatic species to some extent, it likely includes terrestrial organisms in its diet as well. In my opinion, selenium, boron and other constituents discharged from the GDA are the least of this species problems with respect to conservation. Adequate terrestrial habitat in this highly human-influenced landscape is likely the key factor limiting its recovery.

243 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW Is the project design based on the current understanding of the environmental science of selenium? Overall, the GBP monitoring program includes many aspects relevant to our current understanding of selenium bioaccumulation, such as estimates of selenium loading, and selenium concentrations in abiotic (water, sediments) and biotic (invertebrates and vertebrates) components of the various monitoring sites. The notable exceptions are monitoring selenium concentrations in biofilm and eggs as mentioned previously. With all of these data, the GBP has an opportunity to establish a site-specific selenium model for Mud Slough that will allow prediction of a water column selenium level that is protective of aquatic life in this waterbody, which would thus be protective of aquatic life at downstream sites in the San Joaquin River. Excellent guidance is available for taking this next step in monitoring the future recovery of this system (Presser and Luoma 2010). It is also recommended that the GBP personnel read the draft USEPA selenium criterion document, as this contains current state-of-the-science information regarding the aquatic ecotoxicology of selenium. 4. What are the key data that contribute to the better scientific understanding of the behavior of selenium in the system? How can GBP datasets be modified or improved to be more helpful to other programs (e.g., San Joaquin River Restoration Program, Bay-Delta Restoration Program, and the development of site-specific or tissue-based selenium standards by US EPA)? Most of the answers to this question have been addressed in my comments previously. In summary, it is recommended that an ecosystem-scale, site-specific selenium bioaccumulation model be developed for Mud Slough, which will include determinations of selenium in biofilm and fish eggs in addition to the already established monitoring activities. If and when this model predicts no ecological risk to resident biota in Mud Slough, then it can be inferred that there would be no risk to biota inhabiting downstream sites on the San Joaquin River. 5. Does the Biological Effects Monitoring Program achieve the following? If not, how can it be improved? a. Monitor selenium concentrations across all important media (water, particulates, tissue of different food web species) that contribute to selenium bioaccumulation in ecosystems. Again, fish and amphibian egg selenium concentrations and biofilm selenium concentrations are notable gaps in the monitoring program that should be included. b. Identify at-risk species and their food webs to protect communities from selenium exposure. Several of the native fish species collected during community assessments appear to be listed (although I am not familiar with the designations). It is recommended that certain of these fish species be collected during spawning in order to collect eggs for selenium analysis. If the egg selenium concentration for a certain species is lower than the draft USEPA criterion of 15.8 µg Se/g egg dry weight, then this provides the most accurate prediction of no ecological risk to this species, and by extension to the fish community. c. Determine the environmental risk occurring to fish and wildlife (including protected species such as the giant garter snake and San Joaquin kit fox) in Mud Slough (north) and lower San Joaquin River. The answer to this question has been addressed previously. More focused research on Mud Slough will be critical in assessing ecological risk to protected species. When this waterway recovers to the extent that it does not pose ecological risk, then the problem is solved as long as current engineering practices to manage loading of selenium and other constituents of the GDA continue to be in place.

244 242 GRASSLAND BYPASS PROJECT d. Are there environmental benefits of diminished selenium in other parts of the Grasslands wetland water supply channels and the San Joaquin River? Biological monitoring in potentially improved channels has occurred at Mud Slough (north), upstream of the SLD discharge (Site C), Salt Slough (Site F and F2), and at San Joaquin River at Fremont Ford (Site G). The answer to this question is related to larger scale benefits to the entire San Joaquin watershed. Reduced loading of selenium from the GDA has environmental benefits to downstream areas of the watershed, including San Francisco Bay. See my comments above related to cumulative effects assessment for further information. Since inception of the GBP, there have been significant reductions in selenium loading overall, which has been an important benefit to the ecology of the San Joaquin River and associated wetland ecosystems. e. Is the GBP supporting healthy fish communities within the study area? Does the GBP monitor fish communities and abundance to be effectively integrated within other projects? As mentioned previously, the fish community assessments conducted by the CDFW are an important aspect of the monitoring program. Although potential differences among exposure and reference sites are difficult to assess statistically, it is apparent that diverse fish communities are present at even the high exposure area (Mud Slough). However it cannot be determined whether fish migration among study sites is occurring. It is possible that if fish populations decline in Mud Slough due to toxicity, then this area provides an attractive sink for fish migration due to lower fish densities and thus less competition for food and other resources, and reduced predation risk. Expanded population ecology approaches, such as mark-recapture studies using passive integrated transponder (PIT) tags would be required to get a better assessment of the health of fish communities (such as abundances, diversity, and presence of sensitive species and species-at-risk). Another approach that might be worth considering is the Index of Biotic Integrity (IBI; Karr 1981; Karr 1997), which allows for quantitative assessment of fish community ecology in combination with habitat assessment. f. Does the Biological Effects monitoring accomplish an assessment of the risk to human health from consumption of fish from affected channels? Yes, there is a component of the GBP monitoring program that includes determination of selenium in skinless fish muscle (filets) of fish consumed by sport fishers at sites including Mud Slough. These species include catfish, sunfish and carp. It is unlikely that concentrations of selenium (or other contaminants, but I did not see any data) would pose any threat to human health, even at Mud Slough. Humans, as with other mammals, are relatively tolerant to elevated selenium exposure in the range that would occur if consuming these fish. Conclusions and Recommendations In conclusion, the GBP has established an effective, comprehensive long-term monitoring program to assess exposure of biota to selenium and other constituents discharged from the GDA. The monitoring program has shown that significant reductions in selenium loading and exposure have occurred over the first 19 years of the project, particularly in the past decade. Importantly, discharges of selenium and other constituents have been greatly reduced to surrounding wetlands and the San Joaquin River inhabited by fish and wildlife, and potential ecological risks to animals in these areas are now likely minimal. However, Mud Slough remains the area of greatest impact and it is uncertain whether in the final five years of the GBP that this waterbody can recover to the extent that other areas have with respect to selenium ecorisk. My major recommendations, as discussed previously, are summarized below. 1. Scientific attention and financial resources should be re-allocated to focus primarily on biological moni toring of Mud Slough for the remainder of the GBP. Other sites monitored by the GBP should continue, but perhaps at less frequent intervals. 2. Selenium quantification in biofilm, and eggs collected from fishes and amphibians, should be added to the biological monitoring at Mud Slough. These sample analyses represent major data gaps in the GBP monitoring program.

245 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW A site-specific selenium bioaccumulation model should be developed for Mud Slough. This will be useful for making predictions about future recovery of this waterbody and the ecological risks to organisms that utilize it for habitat. 4. Continued monitoring of Mud Slough should be anticipated beyond the 2019 end-date of the GBP. A site-specific model will aid in simplifying this potential monitoring phase, since aqueous selenium concentrations, with the possibility of occasional (e.g., annual) selenium concentrations in fish eggs, should be sufficient data to predict ecological risk. 5. The GBP monitoring program should consider the use of caged fish experiments as a relevant semi-con trolled approach to assess selenium exposure and effects in Mud Slough. A major advantage of such experiments is that the confounding factor of fish migration is eliminated. 6. The GBP monitoring program should focus more attention on statistical approaches to quantify differences, or lack of differences, in biological responses among sites. The importance of appropriate reference site(s) and sufficient sample sizes are key aspects of this recommendation, as discussed previously. 7. Although fish migration cannot be accounted for, the fish community assessment is a strong aspect of the GBP monitoring program as it addresses the ultimate question in ecological risk assessment. Similar to (6) above, attempts at better quantifying community dynamics among sites should be a priority in order to statistically compare sites. 8. The current laboratory toxicity testing is irrelevant to selenium toxicity. Unless the rationale for continuing this testing is related to other constituents of the GDA discharges (e.g., boron, salts, other trace elements), then these financial resources should be allocated to other initiatives as outlined above. 9. If possible, the GBP monitoring program should consider a classical selenium effects assessment comparing Mud Slough to an appropriate reference site (e.g., Salt Slough). This assessment would quantify dose-response relationships between egg selenium concentrations and the frequency of characteristic selenium-induced larval deformities in fish inhabiting each site. This assessment could potentially be integrated with 60-day caging studies using fathead minnow. References Allert AL, Fairchild JF, May TW, Sappington LC, Darnall N, Wilson M Using on-site bioassays to determine selenium risk to propagated endangered fishes. N. Amer. J. Fish. Mgmt. 26: Fan TWM, Teh SJ, Hinton DE, Higashi RM Selenium biotransformations into proteinaceous forms by foodweb organisms of selenium-laden drainage waters in California. Aquat. Toxicol. 57: Fox GA Practical causal inference for ecoepidemiologists. J. Toxicol. Environ. Health 33: Franz ED, Wiramanaden CIE, Gallego-Gallegos M, Tse JJ, Janz DM, Pickering IJ, Liber K Comparative uptake of selenium by Chironomus dilutus from surface water and sediment/dietary exposure pathways using an in-situ caging method. Ecotoxicol. Environ. Saf. 32: Janz DM, Liber K, Pickering IJ, Wiramanaden CI, Weech SA, Gallego-Gallegos M, Driessnack MK, Franz ED, Goertzen MM, Phibbs J, Tse JJ, Himbeault KT, Robertson EL, Burnett-Seidel C, England E, Gent A Integrative assessment of selenium speciation, biogeochemistry, and distribution in a northern coldwater ecosystem. Integr. Environ. Assess. Manag. 10: Janz DM, DeForest DK, Brooks ML, Chapman PM, Gilron G, Hoff D, Hopkins WD, McIntyre DO, Mebane CA, Palace VP, Skorupa JP, Wayland M Selenium toxicity to aquatic organisms. In: Chapman PM, Adams WJ, Brooks ML, Delos CG, Luoma SN, Maher WA, Ohlendorf HM, Presser TS, Shaw DP, editors. Ecological Assessment of Selenium in the Aquatic Environment. Boca Raton (FL), USA: CRC Press. p Janz DM Selenium. In: Wood CM, Farrell AP, Brauner CJ, editors. Fish Physiology, Volume 31B: Homeostasis and Toxicology of Non- Essential Metals. London: Academic Press. p Karr JR Assessment of biotic integrity using fish communities. Fisheries 6: Karr JR Measuring biological integrity. Pp In G.K. Meffe, C.R. Carroll (eds). Principles of Conservation Biology, 2nd ed. Sinauer, Sunderland, MA. Lemly AD Teratogenic effects of selenium in natural populations of freshwater fish. Ecotoxicol. Environ. Saf. 26: Luoma SN, Presser TS Emerging opportunities in management of selenium contamination. Environ. Sci. Technol. 43:

246 244 GRASSLAND BYPASS PROJECT Maher WA, Roach A, Doblin M, Fan T, Foster S, Garrett R, Möller G, Oram L, Wallschläger D Environmental sources, speciation, and partitioning of selenium. In: Chapman PM, Adams WJ, Brooks ML, Delos CG, Luoma SN, Maher WA, Ohlendorf HM, Presser TS, Shaw DP, editors. Ecological Assessment of Selenium in the Aquatic Environment. Boca Raton (FL), USA: CRC Press. p Ohlendorf HM The birds of Kesterson Reservoir: A historical perspective. Aquat. Toxicol. 57: Oikari A Caging techniques for field exposures of fish to chemical contaminants. Aquat. Toxicol. 78: Palace VP, Doebel C, Baron CL, Evans RE, Wautier KG, Klaverkamp JF, Werner J, Kollar S Caging small-bodied fish as an alternative method for environmental effects monitoring (EEM). Water Qual. Res. J. Can. 40: Phibbs J, Franz E, Hauck DW, Gallego M, Tse JJ, Pickering IJ, Liber K, Janz DM. 2011b. Evaluating the trophic transfer of selenium in aquatic ecosystems using caged fish, X-ray absorption spectroscopy and stable isotope analysis. Ecotoxicol. Environ. Saf. 74: Phibbs J, Wiramanaden CIE, Hauck DW, Pickering IJ, Liber K, Janz DM. 2011a. Selenium uptake and speciation in wild and caged fish downstream of a metal mining and milling discharge. Ecotoxicol. Environ. Saf. 74: Presser TS, Luoma SN A methodology for ecosystem-scale modeling of selenium. Integr. Environ. Assess. Manag. 6: Skorupa JP Selenium poisoning of fish and wildlife in nature: Lessons from twelve real-world experiences. In: Frankenberger WT Jr, Engberg RA, editors. Environmental Chemistry of Selenium. New York (NY), USA: Marcel Dekker. p Spallholz JE On the nature of selenium toxicity and carcinostatic activity. Free Radic. Biol. Med. 17: Stewart R, Grosell M, Buchwalter D, Fisher N, Luoma SN, Mathews T, Orr P, Wang XW Bioaccumulation and trophic transfer of selenium. In: Chapman PM, Adams WJ, Brooks ML, Delos CG, Luoma SN, Maher WA, Ohlendorf HM, Presser TS, Shaw DP, editors. Ecological Assessment of Selenium in the Aquatic Environment. Boca Raton (FL), USA: CRC Press. p Young TF, Finley K, Adams WJ, Besser J, Hopkins WD, Jolley D, McNaughton E, Presser TS, Shaw DP, Unrine J Appendix A: Selected case studies of ecosystem contamination by Se. In: Chapman PM, Adams WJ, Brooks ML, Delos CG, Luoma SN, Maher WA, Ohlendorf HM, Presser TS, Shaw DP, editors. Ecological Assessment of Selenium in the Aquatic Environment. Boca Raton (FL), USA: CRC Press. p CHAPTER 3 - REVIEW BY HARRY OHLENDORF Introduction The Grassland Bypass Project (GBP) has operated since 1996 pursuant to a series of agreements that have allowed the San Luis and Delta-Mendota Water Authority (Authority) to use about 28 miles of the lower San Luis Drain (Drain) to convey subsurface agricultural drainwater through adjacent federal and state wildlife management areas to Mud Slough, a tributary to the San Joaquin River. This drainage previously flowed through a variety of channels to wetland habitats in the wildlife areas and the Grassland Water District before discharging to the San Joaquin River. The history of the GBP as well as purposes and objectives of the third Use Agreement for continuation of the GBP in 2010 through 2019 are described in the Final GBP Environmental Impact Statement and Environmental Impact Report (FEIS/EIR; Entrix 2009). The current purposes and objectives are to: extend the San Luis Drain Use Agreement to allow the Grassland Basin Drainers time to acquire funds and develop feasible drainwater treatment technology to meet revised Basin Plan objectives and Waste Discharge Requirements (WDRs) by December 31, 2019; continue the separation of unusable agricultural drainage water discharged from the Grassland Drainage Area (GDA) from wetland water supply conveyance channels for the period ; and facilitate drainage management that maintains the viability of agriculture in the Project Area and promotes continuous improvement in water quality in the San Joaquin River. Section 15.2 of the FEIS/EIR (Entrix 2009) describes the monitoring and reporting program for the GBP. This program is designed to meet the objectives of the comprehensive monitoring program required in Section V of the Use Agreement (Reclamation and Authority 2009; see below).

247 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 245 In association with approval of the proposed continuation of the GBP, the U.S. Bureau of Reclamation (Reclamation) and the Authority requested formal consultation with the U.S. Fish and Wildlife Service (USFWS) on the potential effects of the project to listed species. The request focused primarily on potential effects to the endangered San Joaquin kit fox (Vulpes macrotis mutica) and the threatened giant garter snake (Thamnophis gigas). The USFWS provided its response in its Biological Opinion of December 2009 (USFWS 2009). Critical habitat has not been designated for either of those species, which are discussed below in response to Question 2. USFWS also provided comments relative to project effects on the threatened Delta smelt (Hypomesus transpacificus), which also is discussed below under Question 2. The California Regional Water Quality Control Board, Central Valley Region (Regional Board) issued updated WDRs in 2015 for the Authority and Reclamation surface water discharges from the GBP as Order R (Regional Board 2015). Requirements in the Order implement the Water Quality Control Plan (Basin Plan) for the Sacramento River and San Joaquin River Basins (Regional Board 2011) with respect to the GBP. The Basin Plan designates beneficial uses, establishes water quality objectives, and contains implementation plans and policies for waters of the Sacramento and San Joaquin Basins. The beneficial uses of Mud Slough (north), as identified in the Basin Plan, include limited irrigation supply, stock watering, water contact recreation and noncontact water recreation, sports fishing, shellfish harvesting, warm water aquatic habitat, warm water spawning and wildlife habitat. According to the Order (Regional Board 2015), p. 13: The discharge from the San Luis Drain shall not cause or contribute to the following in Mud Slough (north) or the San Joaquin River. a. In surface water, an exceedance of applicable water quality objectives or a trend of degradation that may threaten applicable beneficial uses, or cause or contribute to a condition of pollution or nuisance.... and g. Toxic pollutants to be present in the water column, sediments or biota in concentrations that adversely affect beneficial uses; that produce detrimental physiological response in human, plant, animal, or aquatic life; or that bioaccumulate in aquatic resources at levels which are harmful to human health. Attachment B of the Order describes the monitoring and reporting requirements for surface water discharges from the GBP as components of the WDRs. On p. 12 of Attachment B, with reference to the sediment monitoring plan, the text states Within six months of this Order s approval, the Dischargers shall submit a sediment monitoring plan for Executive Officer approval. The plan shall include the constituents to be analyzed in the annual sampling event and the schedule for sampling. At a minimum, sediment analysis shall include total selenium. That plan was not available for review (because it was not due to the Regional Board until the end of January 2016), but the review considered other information relative to sediment monitoring that was available (e.g., sediment selenium concentrations, sediment toxicity testing). (Note: After these comments were submitted, the Plan has been submitted to the Regional Board and is available for review.) The current (2009) Use Agreement (No. 10-WC ; Reclamation and Authority 2009) and the previous one (No. 01-WC ; Reclamation and Authority 2001) established the terms and conditions for using the Drain and operation of the GBP. They include monthly and annual load objectives, plus significant fines for exceeding these limits, and have monitoring requirements for the Authority to continue using the Drain. According to Section V of the current Agreement (Reclamation and Authority 2009) and the Record of Decision (Reclamation 2009), the objectives of the comprehensive monitoring program are to provide the following information: water quality data for purposes of determining the Draining Parties compliance with Selenium Load Values and Salinity Load Values as set forth in this Agreement; biological data to allow an assessment of whether any environmental impacts constitute Unacceptable Adverse Environmental Effects that have resulted from this Agreement; and data on sediment levels, distribution, and selenium content. Specifics of the monitoring and reporting program (which includes contaminant monitoring in the Drain, Mud Slough, and the San Joaquin River; acute and chronic toxicity monitoring in Mud Slough; sediment monitoring; and storm water monitoring) are provided in a series of monitoring plans (e.g., Reclamation et al. 2002, 2013, 2015; Reclamation 2011) and annual reports (e.g., San Francisco Estuary Institute [SFEI] 2010, 2011, 2015; Grassland Bypass Project Oversight Committee 2013). The recent reports (e.g., Grassland Bypass Project Oversight Committee 2013; SFEI 2015) provide helpful compilations of data and comparisons toward meeting the environmental commitments defined for continued use of the Drain and the associated monitoring program.

248 246 GRASSLAND BYPASS PROJECT This chapter provides my review of the GBP environmental monitoring program specifically focused on the control and reduction of selenium in the Grasslands wetlands water supply channels and the lower San Joaquin River. It encompasses surface water, biological and sediment monitoring, but excludes groundwater monitoring that is required under the various monitoring programs. The purpose of this review is to evaluate the current environmental monitoring program and the data collected to date, and to provide recommendations for improvements in monitoring for the duration of the GBP through The scope of this review includes the areas directly affected by the GBP (the Drain between Russell Avenue and the terminus, Mud Slough (north) from Kesterson Reservoir to the San Joaquin River, and the San Joaquin River between Fremont Ford and Crows Landing). It does not include regional drainage management projects in the GDA, such as the San Joaquin River Improvement Project (SJRIP) and the San Luis Demonstration Treatment Facility (DTF). Although implementation of those projects will affect the success of the GBP, they are regulated by the 2009 Record of Decision and Biological Opinion for the GBP (Reclamation 2009; USFWS 2009), 2007 Record of Decision (Reclamation 2007) and Biological Opinion (USFWS 2006) for the San Luis Unit Feature Re-evaluation, and the 2012 Biological Memorandum for the DTF (USFWS 2012). The chapter provides my general observations, responses to key questions provided by SFEI to guide feedback in regard to important management issues the GBP seeks to answer, and conclusions and recommendations from the review. General Observations The GBP has operated since 1996 under a series of agreements for use of the Drain to discharge subsurface drainage from the GDA through Mud Slough (north) while removing discharges from wetland channels supplying water to state and federal wildlife areas and wetlands in the Grassland Water District. Effects of the GBP have been monitored under comprehensive environmental programs that have provided data on selenium concentrations in surface water, biota, and sediment for evaluation of the Project. Monitoring locations and specifics of the monitoring/sampling have varied somewhat through time on the basis of changing requirements and evaluation of monitoring results. Overall, the available datasets for the locations affected by the GBP and comparable data for upstream reference locations are very comprehensive. Inclusion of historic data in each of the annual reports facilitates understanding of the comprehensive data. Some of the monitoring data (such as tissue analyses for fish and invertebrates) are particularly useful, while other parts of the monitoring program (such as fish community assessment and toxicity testing) are less useful with respect to selenium. These observations are described in more detail in response to the posed questions below. Responses to Key Questions Responses to key questions provided by SFEI to guide feedback in regard to important management issues the GBP seeks to answer are provided below. 1. Is the GBP monitoring program effectively tracking the consequences (i.e., biological effects) of salt and selenium discharges to Mud Slough (north) (i.e., Stations D, I [I2], and E) and the lower San Joaquin River (Station H [R] and N)? Is it effectively tracking potential biological effects downstream of the Merced River confluence (i.e., Station N)? The monitoring program includes several components that indicate the potential for biological effects of selenium discharges to these reaches, as reported for surface water, biota, and sediment selenium concentrations in various annual monitoring reports (e.g., SFEI 2010, 2011, 2015; Grassland Bypass Project Oversight Committee 2013). The reporting of selenium concentrations in these media is consistent with requirements of the monitoring plans discussed above. Selenium concentrations in biota give a comprehensive characterization of fish and bird exposure to selenium through the food web and of bioaccumulation in their tissues (wholebody fish or bird eggs); those results of the monitoring program are most useful in assessing the potential for effects in the exposed biota. The potential effects of the selenium concentrations in biota can be assessed by comparisons of concentrations in diet (e.g., invertebrates, plant seeds) and the receptors (e.g., as measured in whole-body fish or bird eggs) to levels of concern or toxicity thresholds for fish or birds (as they have been in the annual reports), but actual effects of selenium have generally not been determined. When monitoring/ sampling results indicate a potential for effects in fish but actual effects are uncertain, following a phased approach that includes laboratory studies is generally appropriate for reducing those uncertainties (Janz et al. 2010; Ohlendorf et al. 2011). For example, eggs of selected fish species that are common in the fish community at Station D could be fertilized in the field and then transported to the laboratory, where embryos and larvae would be monitored for effects.

249 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 247 Selenium concentrations in surface water and sediment also are useful for monitoring purposes and the concentrations can similarly be compared to literature-derived effect benchmarks (as they have been in the reports), but assessment of the consequences of those exposures is less direct than for biota selenium. This is because dietary exposure is the most significant exposure pathway for selenium, and tissue concentrations are more interpretable with respect to biological effect concentrations than are those in abiotic media. Comparisons of recent results for selenium concentrations in surface water, biota, and sediment to previous results for each station in each annual report are very useful for tracking temporal changes in selenium levels and evaluating their potential consequences. In contrast, results for the fish community assessments and examinations of fish for anomalies at Stations E and H (as well as G) have shown no trends in composition of the fish community or occurrence of selenium-related anomalies in fish (Grassland Bypass Project Oversight Committee 2013). This is not surprising, given the high variability in community metrics and low probability of finding selenium-related anomalies under site conditions. Short-term toxicity testing of surface water with invertebrates or algae (as has been conducted historically or required by the WDRs) is not very useful for evaluating actual or potential biological effects of selenium discharges to fish, birds, or their food webs. As noted in Chapter 12 of the report (Grassland Bypass Project Oversight Committee 2013), The current toxicity test regime was not designed to characterize potential impacts of selenium to aquatic organisms and wildlife. It was designed to document whether the GDA discharges would result in increased aquatic toxicity in receiving waters. And The observed toxicity may be related to any number or combination of pesticides and other chemicals that entered the surface water system, which consists predominantly of subsurface drain discharges. Similarly, although toxicity testing of sediment may be useful for general monitoring of trends, results likely will be confounded by the presence of other chemicals, an association of effects with selenium concentrations will be uncertain. Although Hyalella azteca (the test organism used for GBP sediment toxicity testing) are more sensitive to waterborne selenium than some other species (e.g., Chironomus sp.), selenium concentrations causing lethality in acute and chronic literature-reported bioassays were >100 µg/l (debruyn and Chapman 2007). I did not find toxicity threshold values for selenium in sediment for Hyalella, and tissue concentrations were neither measured in the GBP test organisms nor did I find threshold values for them in the literature. 2. Is the scope and frequency of monitoring of wetland channels and critical habitat (designated habitat for listed species but critical habitat has not been designated for giant garter snake or San Joaquin kit fox) effective in tracking regulatory commitments? Water quality monitoring of wetland channels has occurred in Salt Slough (Station F, where sediment also is monitored although not required by applicable WDRs), Camp 13 Canal (Station J), Agatha Canal (Station K), San Luis Canal (Station L2), and Santa Fe Canal (Station M2) (see, e.g., Grassland Bypass Project Oversight Committee 2013). Salt Slough is the principal wetland water supply channel for wildlife areas from which drainwater has been removed by the GBP. Station F, located where State Highway 165 crosses Salt Slough, is the monitoring location that reflects selenium concentrations in water for the upstream state and federal wildlife areas, while Stations L2 and M2 characterize inflows to the North Grasslands and Stations J and K do so for inflows to the South Grasslands. Monthly mean selenium concentrations in Salt Slough and the Grassland wetland channels have decreased and usually have met the (monthly mean) objective for fish and wildlife since construction of the bypass. Biota sampling for Salt Slough occurs on the San Luis National Wildlife Refuge at Station F, about 2 miles upstream of where Highway 140 crosses the stream. Selenium concentrations in fish and invertebrates from Salt Slough declined markedly soon after implementation of the GBP and have remained below the toxicity level and mostly below the level of concern. The scope and frequency of monitoring at those locations has been consistent with regulatory commitments.

250 248 GRASSLAND BYPASS PROJECT Critical habitat has not been designated for either the giant garter snake or San Joaquin kit fox (USFWS 2009). Giant garter snakes may occur in permanent aquatic habitat or habitats seasonally flooded during the snakes active season (early-spring through mid-fall), such as marshes, sloughs, ponds, low-gradient streams, irrigation and drainage canals, and rice fields. Giant garter snakes have historically been found in areas potentially affected by GDA discharges (e.g., along Santa Fe Grade), but surveys in 2003 through 2007 (California Department of Fish and Game [CDFG] 2003, 2004, 2007; Hansen 2007, 2008) did not find any occurrences of the species in the potentially affected wetland channels or downstream of discharges to Mud Slough (north). Thus, it is unlikely the GBP would cause significant exposure or adverse effects in the species. However, in its Biological Opinion, USFWS (2009) stated Through requirements of the Service s biological opinion on interim water contract renewals (USFWS 2000a), Reclamation will support studies on selenium impacts to giant garter snakes (USBR 2009). Little is known about the effects of selenium on the giant garter snake. Bioaccumulation of selenium was measured in common garter snakes (Thamnophis sirtalis) exposed in a laboratory study (Sheffield 2006). Snakes receiving a diet of fish that had been fed a selenium-fortified diet accumulated selenium in their blood, but adverse effects on reproduction (typically the most sensitive biological endpoint for egg-laying vertebrates) were not included in the study. In its Biological Opinion, USFWS (2009) mentioned concern about effects of construction activities and selenium bioaccumulation by salt-tolerant crops in the GDA and SJRIP with respect to the San Joaquin kit fox. Monitoring of selenium concentrations in vegetation and small mammals designed to detect potential selenium exposure by kit foxes in those areas began in 2008, and monitoring of blood and hair in coyote was initiated in Levels measured in 2010 and 2011 showed concentrations below concern levels (Grassland Bypass Project Oversight Committee 2013). As mentioned above, the GDA and SJRIP are outside the area considered in this review, and those results were not reviewed in detail. Depending on availability, waterfowl and/or shorebird eggs were collected from areas adjacent to Mud Slough and the Drain in the spring of each year from 1996 through 2011 (Grassland Bypass Project Oversight Committee 2013). The data were evaluated for potential effects on bird reproduction (discussed under other questions) but not as food items for kit foxes. The monitoring program also includes sediment quality and quantity in the Drain. The USFWS (2009) mentioned its objection to disposal of sediments containing selenium at concentrations exceeding 2 mg/kg dry weight to nearby upland open areas because of risk to wildlife foraging in those areas. Those risks may exist for terrestrial species, including the kit fox, but a risk assessment for the sediment application to land was beyond the scope of this review. The Reclamation and Authority request for consultation with the USFWS on potential effects of the GBP to listed species indicated that the Delta smelt would not be affected by the proposed action. In its Biological Opinion, the USFWS (2009) reiterated from a 2001 biological opinion that, although Delta smelt do not reach Mud Slough or the San Joaquin River above the Merced River, GBP discharges travel downstream via the San Joaquin River to the Delta and Delta smelt critical habitat, and that the species should be listed under the may affect category. This review considered potential effects in the lower San Joaquin River as reflected by data from Station N, but not into the Delta, as agreed during scoping discussions for the review. Thus, effects on the Delta smelt are similar to those for other species at that location, where recent monthly mean selenium concentrations have been well below the 5.0 µg/l water quality objective (Grassland Bypass Project Oversight Committee 2013). It seems unlikely the species would be adversely affected in its critical habitat. Critical habitat for the California Central Valley Steelhead Distinct Population Segment is located in the San Joaquin River upstream to the Merced River and up that river, but not in the San Joaquin River upstream of that confluence (National Oceanic and Atmospheric Administration [NOAA] 2005). Thus, exposure of steelhead (Oncorhynchus mykiss) would occur mainly downstream of the Merced River confluence and can be evaluated by the data for Station N, where water quality is monitored but selenium concentrations in biota are not. Recent monthly mean selenium concentrations at Station N have been well below the 5.0 µg/l water quality objective (Grassland Bypass Project Oversight Committee 2013), and should not adversely affect the steelhead.

251 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 249 Also, adult steelhead do not feed extensively when they return to fresh water to spawn (NOAA 2005), so the threshold for effects on growth of juvenile salmonids is more relevant than thresholds based on reproductive effects. The monitoring reports (e.g., Grassland Bypass Project Oversight Committee 2013) describe derivation of conservative threshold concentrations for effects in juvenile salmonids, but tissue data are not available from the steelheads critical habitat for evaluation. Also, USEPA (2015) derived a less conservative threshold for reduced growth of juvenile Chinook salmon (Oncorhynchus tshawytscha) fed a selenomethionine-dosed diet (whole-body selenium concentration of 7.36 mg/kg), based on the same study by Hamilton et al. (1990) that was used to derive lower effect concentrations in the monitoring report (Chapter 7). 3. Is the project design based on the current understanding of the environmental science of selenium? The location of monitoring stations (upstream and downstream of discharges; wetland channels) and the frequency of monitoring (more frequent for variable concentrations in water, less frequent for biota and sediment that change more slowly) are consistent with the understanding of selenium behavior in the environment. The monitoring program has included a comprehensive evaluation of selenium concentrations in different invertebrate taxa (including zooplankton at Station I/I2, as shown in Figure 5F of Grassland Bypass Project Oversight Committee 2013, although it is difficult to distinguish different taxa in the figure) and fish species in the affected drainages and established patterns among the trophic levels sampled. Knowing the selenium concentrations in these diverse biota allows for direct interpretation of the exposure levels and potential for effects in different species and trophic levels and for monitoring of temporal trends. The focus on exposures of fish and birds as well their diet is consistent with the environmental science of selenium. Monitoring of particulates to make the linkage between waterborne selenium concentrations and those in the lowest trophic levels of invertebrates would provide more information about the bioaccumulation of selenium (consistent with Presser and Luoma 2010, for example), but is not necessary for evaluating potential effects, because of the direct interpretability of the monitoring data to assess risk. Fish community assessments and examinations of fish for anomalies are sometimes useful for selenium assessment if reproductive effects are expected or they are severe (Janz et al. 2010; Ohlendorf et al. 2011), and they have been included in the comprehensive monitoring program. However, monitoring at Stations E, G. and H has shown no trends in composition of the fish community or occurrence of selenium-related anomalies in fish (Grassland Bypass Project Oversight Committee 2013). This is not surprising, given the high variability in community metrics and low probability of finding selenium-related anomalies under site conditions, as noted above in response to Question What are the key data that contribute to the better scientific understanding of the behavior of selenium in the system? How can GBP datasets be modified or improved to be more helpful to other programs (e.g., San Joaquin River Restoration Program, Bay-Delta Restoration Program, and the development of site-specific or tissue-based selenium standards by USEPA)? The key data are the multi-media monitoring results (i.e., in water, biota, and sediment) from multiple stations since the GBP was implemented in The comprehensive, long-term monitoring program supports understanding of selenium sources, transport through the Drain and wetland channels, and bioaccumulation in fish, birds, and their food webs. The unique dataset available from the GBP monitoring program also facilitates understanding temporal associations of selenium concentrations among different trophic levels of biota and those in water (e.g., Beckon 2014), which contributes substantially to understanding of selenium behavior in this system. Levels of concern and toxicity thresholds for interpretation of results and prediction of risk (i.e., potential effects) are fairly well established for fish and birds. Information also is available for amphibians (bullfrog tadpoles; Lithobates catesbeianus) at selected monitoring stations and the data are useful for monitoring temporal trends, but effect levels are less well established for amphibians than for fish or birds (Janz et al. 2010), so the monitoring data are not readily assessed for prediction of risk to amphibians.

252 250 GRASSLAND BYPASS PROJECT The available monitoring data (e.g., as reported and summarized in Grassland Bypass Project Oversight Committee 2013) should be useful to other programs having an interest in the spatial patterns or temporal trends of selenium concentrations associated with the GBP (such as San Joaquin River Restoration Program and Bay-Delta Restoration Program). They can be used to evaluate the potential for adverse effects in fish and birds inhabiting the areas receiving GDA drainage or in areas from which the drainage has been removed (as reflected by data for wetland channels and associated biota from Station F) and similarly for humans eating fish from the drainages. Selenium concentrations in invertebrates (as dietary items for fish or birds), wholebody fish, or bird eggs in Mud Slough (including the backwater at Station I/I2) often exceed levels of concern and indicate the potential for adverse effects in fish and birds, whereas the risks of effects in other wetlands have been greatly reduced. Samples of carp (Cyprinus carpio) muscle collected at Station E, but not at Stations G or H, have sometimes exceeded the 2 mg/kg (wet weight) screening level for human health protection in recent years (based on California Office of Environmental Health Hazard Assessment [OEHHA] 2008; SFEI 2011). These muscle samples from Stations E and H are considered to be representative of fish that would be eaten by people fishing in areas downstream of the GBP discharge. The frequency of exceedance has been about 10 percent in the carp samples from Station E since implementation of the GBP (SFEI 2011; Grassland Bypass Project Oversight Committee 2013). If there is a concern about actual effects (e.g., to satisfy the receiving water limitation on p. 13 in the Order [Regional Board 2015] that states The discharge from the San Luis Drain shall not cause or contribute to the following in Mud Slough (north) or the San Joaquin River... Toxic pollutants to be present in the water column, sediments or biota in concentrations that adversely affect beneficial uses; that produce detrimental physiological response in human, plant, animal, or aquatic life (emphasis added); or that bioaccumulate in aquatic resources at levels which are harmful to human health. ), more detailed toxicological/effect studies are needed. Similarly, if more detailed information is needed for development of site-specific or tissue-based selenium standards by USEPA, it may be useful to include analyses of particulate selenium in the water column concurrently with water and biota sampling at locations where both water and biota are sampled for selenium analysis. Although bioaccumulation modeling can be done without including particulates, they were included in the USEPA (2015) modeling conducted for development of the draft aquatic life ambient water quality criterion for selenium and likely would be used by USEPA for development or future modification of site-specific or tissue-based selenium standards. 5. Does the Biological Effects Monitoring Program achieve the following? If not, how can it be improved? a. Monitor selenium concentrations across all important media (water, particulates, tissue of different food web species) that contribute to selenium bioaccumulation in ecosystems. Although particulates (e.g., suspended particulates filtered from the water column, algae, or phytoplankton) are not sampled, the inclusion of this matrix in the monitoring program is not necessary to understand exposure and potential risk of selenium effects in fish, birds, or humans. This is because concentrations measured in fish (whole-body or muscle) and birds (eggs) as well as their food webs (invertebrates and plant seeds) allow for direct comparisons to levels of concern or toxicity thresholds for effects in the important endpoint receptors. If there is an interest in modeling selenium bioaccumulation in the ecosystem (i.e., from water to endpoint receptors or the reverse thereof, such as in Presser and Luoma 2010), monitoring of particulates would be essential. b. Identify at-risk species and their food webs to protect communities from selenium exposure. Yes, the monitoring program is very comprehensive and identifies all of these for evaluation of potential effects/risk. In fact, as noted in Conclusions and Recommendations, the number of invertebrate taxa and fish species that are analyzed could be reduced somewhat without substantially decreasing the ability to detect spatial patterns and temporal changes associated with GBP discharges. If it is necessary to understand actual effects on the at-risk species, additional studies would be required, as noted elsewhere in this chapter.

253 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 251 c. Determine the environmental risk occurring to fish and wildlife (including protected species such as the giant garter snake and San Joaquin kit fox) in Mud Slough (north) and lower San Joaquin River. Yes, direct measurement of selenium concentrations in whole-body fish and in bird eggs as well as fish and bird food webs (invertebrates and plant seeds) allows for direct comparisons to levels of concern or toxicity thresholds for effects in the important endpoint receptors. In this way environmental risk can be predicted and changes through time can be determined by differences in the frequency of exceedance of the benchmarks used for evaluation. The levels of concern and toxicity thresholds used in the monitoring program are conservative, so they should be protective for the receptor species. Please see response to Question 2 about giant garter snake, San Joaquin kit fox, and other protected species. d. Are there environmental benefits of diminished selenium in other parts of the Grasslands wetland water supply channels and the San Joaquin River? Biological monitoring in potentially improved channels has occurred at Mud Slough (north), upstream of the SLD discharge (Site C), Salt Slough (Site F and F2), and San Joaquin River at Fremont Ford (Site G). Yes, the environmental benefits of diminished selenium concentrations are reflected by monitoring data from wetland channels and the San Joaquin River. Selenium concentrations in water at all locations from which high-selenium drainage water was removed, in fish and invertebrates from Salt Slough (Station F), as well as in fish from the San Joaquin River (Station G) declined rapidly after implementation of the GBP and have remained low, only occasionally exceeding the level of concern (Grassland Bypass Project Oversight Committee 2013). Please see also response to Question 2 for other comments about monitoring of the wetland channels. e. Is the GBP supporting healthy fish communities within the study area? Does the GBP monitor fish communities and abundance to be effectively integrated within other projects? The health of fish communities within the study area is uncertain. Fish community assessments have been conducted since 1993 in Mud Slough at Highway 140 (Station E) and in the San Joaquin River at Fremont Ford (Station G) and below Mud Slough (Station H) to describe species richness, abundance and community structure (Grassland Bypass Project Oversight Committee 2013). Fish assemblages from these sites were compared both spatially and temporally to determine whether conditions for fish species in the San Joaquin River improved and conditions in Mud Slough degraded. Because the GBP began operation in 1996, this sampling schedule was intended to provide a before-and-after characterization of the fish communities at these sites. No time trends are apparent in fish species assemblages during 1993 to 2011 at these locations, and no time trend is evident in total anomalies for the various groups of fishes at each site. After 15 years of Project operation, no clear pattern of temporal or geographic variation in fish community structure attributable to the Project has emerged. However, as noted in the report, current methods of assessing fish species assemblages may lack the power to detect all but the most pronounced alterations in community structure. f. Does the Biological Effects monitoring accomplish an assessment of the risk to human health from consumption of fish from affected channels? Adequacy of monitoring data to assess risk to human health from consumption of fish from affected channels should be determined by OEHHA, because that agency has particular requirements for adequacy of data. About 10 percent of the more than 120 samples of carp muscle collected from Mud Slough at Highway 140 (Station E) have exceeded the 2 mg/kg (wet weight) screening level for human health protection in recent years. In contrast, selenium concentrations in carp muscle samples from the San Joaquin River at Fremont Ford upstream of Mud Slough (north) (Station G) and San Joaquin River at Hills Ferry (Station H) have not exceeded the screening level. The carp muscle samples from Stations E and H are considered to be representative of fish that would be eaten by people fishing in areas downstream of the GBP discharge.

254 252 GRASSLAND BYPASS PROJECT Conclusions and Recommendations Comprehensive monitoring programs have provided large datasets for evaluation of the environmental effects of the GBP since it was implemented in Selenium concentrations in surface water, biota, and sediment have been measured through time, and they provide a basis for comparing locations affected by the GBP to conditions in upstream reference locations. Sampling of water and sediment for selenium analyses is more straightforward and less effort than that for biota sampling. Continuing monitoring of those media in accordance with the 2015 monitoring plan (Reclamation et al. 2015) should meet the requirements of the Use Agreement (Reclamation and Authority 2009) and WDRs (Regional Board 2015). I recommend that approach. Monitoring data for invertebrates, fish, and bird eggs are particularly useful for evaluating potential adverse effects from selenium. Available data provide a good understanding of trophic level and inter-taxa (invertebrate) or inter-species (fish) differences. Those data should be evaluated toward streamlining the analyses for selenium. I recommend consideration of reducing the frequency of sampling to less than quarterly by focusing on the most important season, which, for selenium, would be the time when egg development is occurring. It seems possible that sampling twice a year would meet the monitoring goals for detecting spatial patterns and temporal trends. Available data also should be reviewed to determine if a subset of invertebrate taxa and fish species would provide sufficient data for monitoring spatial patterns and temporal trends to meet the objectives of monitoring. It seems likely that representative taxa/species could be identified for analyses, and the other samples could be archived for possible future analyses, if they were warranted. Monitoring of bird eggs also should be continued, consistent with the 2015 plan (Reclamation et al. 2015). If more detailed information is needed for development or future modification of site-specific or tissue-based selenium standards by USEPA, I recommend including analyses of particulate selenium in the water column concurrently with water and biota sampling at locations where those media are sampled for selenium analysis. Although bioaccumulation modeling can be done without including that trophic level, it likely would be used for development or modification of site-specific or tissue-based selenium standards by USEPA in the longer timeframe (it would not be helpful in the shorter timeframe, if USEPA develops standards within the next year, as expected). Cost savings realized from streamlining the biota monitoring effort (as suggested above) could be used to support the analyses of particulates. The potential effects of the selenium concentrations found in biota can be assessed by comparisons of concentrations in diet (e.g., invertebrates, plant seeds) and the higher trophic-level receptors (e.g., as measured in whole-body fish or bird eggs) to levels of concern or toxicity thresholds for fish or birds (as they have been in the annual reports), but actual effects of selenium have generally not been determined. Selenium concentrations in fish collected at Station D (Mud Slough (north) below the GBP discharge from the Drain) often exceed the level of concern, and sometimes the toxicity threshold. If assessment of potential effects is adequate for meeting goals and objectives for the monitoring, comparisons to the threshold levels should be continued. However, if it is desirable to determine actual effects, I recommend considering laboratory studies with a selected fish species as an approach for reducing uncertainties about effects. For example, eggs of a fish species that is common at Station D and for which adequate husbandry information is available could be fertilized in the field and then transported to the laboratory, where embryos and larvae would be monitored for effects. Because results for the fish community assessments conducted since 1993 have shown no trends in composition of the fish community, I recommend discontinuing fish community assessments, the requirements of the WDRs (Regional Board 2015) notwithstanding. Given the high variability in community metrics and low probability of detecting differences/changes, it seems unlikely that community assessments will be worth the monitoring effort. Although examinations of fish for selenium-related anomalies in fish since 1993 also have shown no trends, fish that are collected for selenium analyses should be examined for anomalies, even though the incidence is likely to be low. Toxicity testing of water with invertebrates, such as has been included in the monitoring program, may be useful for other purposes, but such tests are not very relevant for selenium, in part because of the relative insensitivity of invertebrates. As noted above, the results also are likely to be confounded because of the presence of other chemicals in the water.

255 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 253 Similarly, although toxicity testing of sediment may be useful for general monitoring of trends, results likely will be confounded by the presence of other chemicals, and an association of effects with selenium concentrations will be uncertain. Inclusion of historic data in each of the annual reports facilitates understanding of the comprehensive data. This should be continued in future reports. References Beckon, W How to estimate trophic position of fish from lag in contaminant bioaccumulation. Poster abstracts, p Bay- Delta Science Conference, October 28-30, Sacramento, CA. California Department of Fish and Game (CDFG) Progress Report for the San Joaquin Valley Giant Garter Snake Conservation Project Prepared by Catherine Dickert, Los Banos Wildlife Complex, Los Banos, CA. California Department of Fish and Game (CDFG) Progress Report for the San Joaquin Valley Giant Garter Snake Conservation Project Prepared by Justin Sloan, Los Banos, CA. California Department of Fish and Game (CDFG) San Joaquin Valley Giant Garter Snake Trapping Effort Prepared by CDFG Staff, Los Banos Wildlife Area. July. California Office of Environmental Health Hazard Assessment (OEHHA) Development of Fish Contaminant Goals and Advisory Tissue Levels for Common Contaminants in California Sport Fish: Chlordane, DDTs, Dieldrin, Methylmercury, PCBs, Selenium, and Toxaphene. Oakland: California Environmental Protection Agency. California Regional Water Quality Control Board, Central Valley Region (Regional Board) The Water Quality Control Plan (Basin Plan) for the California Regional Water Quality Control Board Central Valley Region, Fourth Edition. Revised October 2011 (with Approved Amendments). Available at California Regional Water Quality Control Board, Central Valley Region (Regional Board) Order R ; Waste Discharge Requirements for San Luis & Delta-Mendota Water Authority and United States Department of the Interior Bureau of Reclamation, Surface Water Discharges from the Grassland Bypass Project. July 31. debruyn, A.M., and P.M. Chapman Selenium toxicity to invertebrates: Will proposed thresholds for toxicity to fish and birds also protect their prey? Environmental Science and Technology 41: Entrix Grassland Bypass Project, Environmental Impact Statement and Environmental Impact Report. Final. State Clearing House No Prepared for U.S. Bureau of Reclamation and San Luis & Delta-Mendota Water Authority by Entrix; Concord, CA. August. Grassland Bypass Project Oversight Committee. (2013). Grassland Bypass Project Annual Report Contribution No San Francisco Estuary Institute. Richmond, CA. Available at Hamilton, S.J., K.J. Buhl, N.L. Faerber, R.H. Wiedmeyer, and F.A. Bullard Toxicity of organic selenium in the diet to Chinook salmon. Environmental Toxicology and Chemistry 9: Hansen, E.C Implementation of Priority 1 Recovery Tasks for the Giant Garter Snake (Thamnophis gigas) in Merced County, California. Prepared for U.S. Fish and Wildlife Service, Sacramento, CA. April 15. Hansen, E.C Implementation of Priority 1, Priority 2, and Priority 3 Recovery Tasks for Giant Garter Snake (Thamnophis gigas) Continuing Surveys in Merced County, California, with an Expansion to Northern Fresno County. Prepared for U.S. Fish and Wildlife Service, Sacramento, CA. May 1. Janz, D.M., D.K. DeForest, M.L. Brooks, P.M. Chapman, G. Gilron, D. Hoff, W.A. Hopkins, D.O. McIntyre, C.A. Mebane, V.P. Palace, J.P. Skorupa, and M. Wayland Selenium toxicity to aquatic organisms. Ecological Assessment of Selenium in the Aquatic Environment. Pp Eds. P.M. Chapman, W.J. Adams, M.L. Brooks, C.G. Delos, S.N. Luoma, W.A. Maher, H.M. Ohlendorf, T.S. Presser, and D.P. Shaw. Boca Raton, FL: CRC Press. Ohlendorf, H.M., S.M. Covington, E.R. Byron, and C.A. Arenal Conducting site-specific assessments of selenium bioaccumulation in aquatic systems. Integrated Environmental Assessment and Management 7: National Oceanic and Atmospheric Administration (NOAA) CFR Part 226; Endangered and Threatened Species; Designation of Critical Habitat for Seven Evolutionarily Significant Units of Pacific Salmon and Steelhead in California; Final Rule. Federal Register Vol. 70, No. 170: September 2.

256 254 GRASSLAND BYPASS PROJECT Presser, T.S., and S.N. Luoma A methodology for ecosystem-scale modeling of selenium. Integrated Environmental Assessment and Management 6: San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report Richmond, CA. July. Available at San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report Richmond, CA. October. Available at San Francisco Estuary Institute (SFEI) Grassland Bypass Project Annual Report Partial Draft. Richmond, CA. Available at U.S. Bureau of Reclamation (Reclamation) San Luis Drainage Feature Re-evaluation, Final Environmental Impact Statement, Record of Decision. Mid-Pacific Region, Sacramento, CA. March 6. U.S. Bureau of Reclamation (Reclamation) Record of Decision. Grassland Bypass Project, ROD South-Central California Area Office, Fresno, CA. December. U.S. Bureau of Reclamation (Reclamation) Grassland Bypass Project 2011 Interim Water Quality Monitoring Program. May 23. U.S. Bureau of Reclamation and San Luis & Delta-Mendota Water Authority (Reclamation and Authority) Agreement for Use of the San Luis Drain for the Period October 1, 2001 through December 31, Agreement No. 01-WC U.S. Bureau of Reclamation and San Luis & Delta-Mendota Water Authority (Reclamation and Authority) Agreement for Continued Use of the San Luis Drain for the Period January 1, 2010 through December 31, Agreement No. 10-WC December 17. U.S. Bureau of Reclamation, et al. (Reclamation et al.) Monitoring Program for the Operation of the Grassland Bypass Project. June. Prepared by the Grassland Bypass Project Data Collection and Review Team. Available at U.S. Bureau of Reclamation, et al. (Reclamation et al.) Grassland Bypass Project 2013 Revised Monitoring Program for the Continued Operation of the Grassland Bypass Project January 1, December 31, Data Collection and Reporting Team Final. Revised March 26, Prepared by the Data Collection and Reporting Team for the Grassland Bypass Project: U.S. Bureau of Reclamation, U.S. Environmental Protection Agency, U.S. Fish and Wildlife Service, U.S. Geological Survey, Central Valley Regional Water Quality Control Board, California Department of Fish and Game, San Luis & Delta-Mendota Water Authority. Available at gov/mp/grassland/documents/gbp_2013_rev_mon_plan.pdf. U.S. Bureau of Reclamation, et al. (Reclamation et al.) Grassland Bypass Project 2015 Environmental Monitoring Program September 1, December 31, Data Collection and Reporting Team Draft. Revised 14 August Prepared by the Data Collection and Reporting Team for the Grassland Bypass Project: U.S. Bureau of Reclamation, U.S. Environmental Protection Agency, U.S. Fish and Wildlife Service, U.S. Geological Survey, Central Valley Regional Water Quality Control Board, California Department of Fish and Wildlife, San Luis & Delta-Mendota Water Authority. U.S. Environmental Protection Agency (USEPA) Draft Aquatic Life Ambient Water Quality Criterion for Selenium Freshwater Office of Water, Washington, D.C., EPA 822-P July. U.S. Fish and Wildlife Service (USFWS) Fish and Wildlife Coordination Act Report, San Luis Drainage Feature Re-evaluation Project. Sacramento Fish and Wildlife Office, Sacramento, CA. May 16. U.S. Fish and Wildlife Service (USFWS) Endangered Species Consultation on the Proposed Continuation of the Grassland Bypass Project, Sacramento Fish and Wildlife Office, Sacramento, CA. December 18. U.S. Fish and Wildlife Service (USFWS) San Luis Drainage Feature Re-evaluation Demonstration Treatment Facility at Panoche Drainage District. Sacramento Fish and Wildlife Office. Sacramento, CA. June 4.

257 CHAPTER 12: GRASSLAND BYPASS PROJECT PEER REVIEW 255 About the Reviewers Dr. Thomas Grieb is a principal scientist and director of the Research & Development Group at Tetra Tech, Inc. with 40 years experience. He received his B.A. in Zoology from the University of California, Berkeley and M.A. degrees in Marine Biology from San Francisco State University and Biostatistics from the University of California Berkeley. He received his Ph.D. from the University of California, Berkeley in Environmental Health Science. He recently served as project manager for technical efforts that supported the preparation of the Selenium TMDL by the California Regional Water Quality Control Board. This work included source characterization and selenium loading assessment, assessment of the toxicological effects of selenium on biota, the development of a conceptual model of the processes that affect selenium biogeochemistry, and the modeling of selenium fate and transport in the Bay-Delta. His primary research interests include the behavior of metals in the aquatic environment and the application of statistical methods to characterize uncertainty in environmental datasets and simulation models. Prof. Dr. David Janz grew up in Vancouver, BC, Canada and was educated at Simon Fraser University (B.Sc. Ecology, 1987), Trent University (M.Sc. Watershed Ecosystems, 1991) and the University of British Columbia (Ph.D. Pharmacology and Toxicology, 1995). After postdoctoral training at the University of Guelph, he was an Assistant Professor in the Department of Zoology, Oklahoma State University from In 2002, he joined the faculty in Veterinary Biomedical Sciences, University of Saskatchewan, where he was promoted to Professor in His academic position is closely associated with the Toxicology Centre at the University of Saskatchewan, where he is currently Associate Director (Academic) and Chair of the Toxicology Graduate Program. Prof Janz s research program focuses on how environmental stressors such as toxicants interact with physiological processes in vertebrate animals, primarily aspects of developmental biology and reproductive endocrinology. Although fish have always been his primary animal model, he has also published research conducted in amphibians, reptiles, birds, and mammals. Since 2005, a major focus of his research program has been on the aquatic ecotoxicology of selenium, where he has published over 30 peer-reviewed journal articles and book chapters on this topic, including three Highlighted Articles in the journal Ecotoxicology and Environmental Safety, and the 2014 Best Paper Award in the SETAC journal Integrated Environmental Assessment and Management. Dr. Harry Ohlendorf has been employed at CH2M HILL since 1990 and is a Certified Wildlife Biologist. He received his undergraduate and graduate degrees from Texas A&M University, including a B.S. in Wildlife Management (Fisheries Option) in 1962, an M.S. in Wildlife Science in 1969, and his Ph.D. in Wildlife Science in At CH2M HILL, he manages or provides technical oversight for a wide variety of environmental projects, including the planning, implementation, and reporting of site ecological characterizations and surveys, contaminant exposure and effect analyses, risk characterization, and project impact evaluations. He provides firm-wide technical guidance in the area of ecological risk assessment and risk management. Recent projects include the application of wildlife toxicology knowledge to projects for government (e.g., California Department of Water Resources; USFWS; USEPA; USDOE; U.S. Army, Air Force, and Navy) and private-sector (e.g., oil refinery, coal and metal mining, chemical manufacturing) clients in a wide variety of environmental settings. Dr. Ohlendorf began his career with the U.S. Fish and Wildlife Service's Patuxent Wildlife Research Center in Laurel, Maryland, where he served for 7 years as assistant director of the Research Center and was actively involved in pollution ecology research. Subsequently, he was leader of the Center s Pacific Coast Research Station in Davis, California, and studied the pollution ecology of wildlife. For 18 years, Dr. Ohlendorf's research for the USFWS focused on the occurrence and impacts of contaminants in aquatic and terrestrial ecosystems. Ecotoxicology of selenium is one of Dr. Ohlendorf s specialties. He has been recognized as one of the "Pioneers of Selenium Research" in a book, Environmental Chemistry of Selenium (edited by W.T. Frankenberger, Jr., and R.A. Engberg; Marcel Dekker, Inc., 1998), and was a co-editor of Ecological Assessment of Selenium in the Aquatic Environment (along with P.M. Chapman, et al; CRC Press, 2010). He has authored numerous related technical papers and book chapters. His current interests also focus particularly on the importance of doing well-planned, relevant studies of the effects of environmental contaminants in fish and wildlife, and application of the results of those studies to environmental decision-making. Dr. Ohlendorf has been a member of The Wildlife Society s Wildlife Toxicology Working Group since it was formed, and has served as Chair of the Group.