Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report

Transcription

1 Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report Prepared for: Yuba County Water Agency 1220 F Street Marysville, CA Contact: Curt Aikens 530/ Prepared by: ICF Jones & Stokes 630 K Street, Suite 400 Sacramento, CA Contact: Bill Mitchell 916/ April 2009

2 ICF Jones & Stokes Lower Yuba River redd dewatering and fry stranding study 2008 annual report. Final. April. (ICF J&S ) Sacramento, CA. Prepared for: Yuba County Water Agency.

3 Contents Page Introduction... 1 Background... 1 Objectives... 3 Approach... 3 Study Tasks... 5 Yuba Project Area and Facilities... 6 New Bullards Bar Reservoir... 7 Englebright Reservoir... 7 Lower Yuba River... 8 Operations Objectives... 8 Base Flow Operations... 9 Storm Runoff Operations... 9 Flood Control Operations Yuba Project Area Hydrology Chinook Salmon and Steelhead Life History Chinook Salmon Steelhead Habitat Mapping Fish Stranding Surveys Methods Results Summary and Recommendations Literature Cited Appendix A Data Summary Tables Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report i April 2009 J&S

4 Tables Follows Page 1 Table 1. Status of Study Tasks... on page 5 2 Dates of Aerial Photographs and Mean Daily Flows... on page 13 3 Results of Bar Stranding Surveys Following Nighttime Flow Reduction of 1,400 to 1,150 cfs (measured at Smartville gage) on June 1, Off-Channel Sites Identified as Potential Fish Stranding Sites before the Flow Reduction on June 1, Off-Channel Sites Disconnected from Main River by Flow Reduction on June 1, Results of Long-Term Monitoring of Off-Channel Sites Following Flow Reduction on June 1, Stranding Evaluations and Flow Conditions Evaluated in 2007 and on page 20 Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report ii April 2009 J&S

5 Figures Follows Page 1 Redd Dewatering Fry Stranding (Beaching) Fry Stranding (Isolation) Seasonal Operations Objectives of the Yuba Project Average Monthly Flows (cfs) Lower Yuba River at Smartville and Marysville Gages Typical Range of Flows and Probability of Exceedance in Lower Yuba River by Month Typical Range of Anticipated Yuba River Flows Under the Yuba River Accord Exceedance Probability of Historical Mean Daily Yuba River Flows in October ( ) Exceedance Probability of Historical Mean Daily Yuba River Flows in March ( ) Likelihood of Controlled Flows Historical Daily Average Yuba River Stage at Smartville and Marysville (WY 2001) Historical Daily Average Yuba River Stage at Smartville and Marysville (WY 2006) General Timing and Relative Abundance of Chinook Salmon Spawning, Incubation, and Fry Rearing Life Stages General Timing and Relative Abundance of Steelhead Spawning, Incubation, and Fry Rearing Life Stages Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report iii April 2009 J&S

6 14 General Timing and Relative Abundance of Steelhead Spawning, Incubation, and Fry Rearing Life Stages Mean Daily Yuba River Flows Measured at the Smartville and Marysville Gages in 2007 and Daily Minimum and Maximum Water Temperatures Measured at Six O-Channel Monitoring Sites Following the June 1, 2008 Flow Reduction Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report iv April 2009 J&S

7 Acronyms and Abbreviations cfs DFG GPS J&S msl NID NMFS NMFS PPC SWRCB USFWS cubic feet per second California Department of Fish and Game global positioning system Jones & Stokes mean sea level Nevada Irrigation District National Marine Fisheries Service National Marine Fisheries Service Power Purchase Contract State Water Resources Control Board U.S. Fish and Wildlife Service Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report v April 2009 J&S

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9 Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report Introduction The following report summarizes progress on the Lower Yuba River Redd Dewatering and Fry Stranding Study through calendar year This year marked the second year of fry stranding surveys to evaluate the effectiveness of flow reduction and fluctuation criteria in minimizing stranding of Chinook salmon and steelhead/rainbow trout fry in the lower Yuba River. This report includes: a review of the regulatory background, study plan development, primary study objectives, conceptual models and analytical approach, and accomplishments to date; a description of the Yuba Project area, hydrology, facilities, and operational objectives relevant to flow fluctuations and reductions; a description of the life history of Yuba River Chinook salmon and steelhead/rainbow trout; the results of 2008 fish stranding surveys; and a summary of results to date and recommendations for future monitoring. Background On March 1, 2001, the State Water Resources Control Board (State Water Board) issued Decision-1644 (D-1644), which includes provisions that limit the magnitude and rate of controlled flow reductions and daily flow fluctuations downstream of Englebright Dam to protect Chinook salmon and steelhead redds and fry. The D-1644 flow reduction and fluctuation criteria are as follows: With the exception of emergencies, flood flows, bypasses of uncontrolled flows into Englebright Reservoir, uncontrolled spilling, or uncontrolled flows of tributary streams downstream of Englebright Dam, permittee shall make reasonable efforts to operate New Bullards Bar Reservoir and Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 1 April 2009 J&S

10 Yuba County Water Agency Englebright Reservoir to avoid fluctuations in the flow of the lower Yuba River downstream of Englebright Dam. Daily changes in project operations affecting releases or bypasses of flow from Englebright Dam shall be continuously measured at the USGS gage at Smartville and shall be made in accordance with the following conditions: a. Project releases or bypasses that increase streamflow downstream of Englebright Dam shall not exceed a rate of change of more than 500 cfs per hour. b. Project releases or bypasses that reduce streamflow downstream of Englebright Dam shall be gradual and, over the course of any 24-hour period, shall not be reduced below 70 percent of the prior day s flow release or bypass flow. c. Once the daily project release or bypass level is achieved, daily fluctuations in the streamflow level downstream of Englebright Dam due to changes in project operations shall not vary up or down by more than 15 percent. d. During the period from September 15 to October 31, permittee shall not reduce the flow downstream of Englebright Dam to less than 55 percent of the maximum release or bypass level that has occurred during the September 15 to October 31 period or the minimum streamflow requirement that would otherwise apply, whichever is greater. e. During the period from November 1 to March 31, permittee shall not reduce the flow downstream of Englebright Dam to less than the minimum streamflow release or bypass established under (d) above; or 65 percent of the maximum flow release or bypass that has occurred during the November 1 March 31 period; or the minimum streamflow requirement that would otherwise apply, whichever is greater. While these criteria are expected to provide increased protection for Chinook salmon (fall- and spring-run) and steelhead, uncertainty regarding the magnitude of potential effects and the factors influencing redd dewatering and fry stranding prompted the need for further evaluation of the proposed flow reduction and fluctuation criteria. In compliance with State Water Board D-1644, Jones & Stokes (J&S), on behalf of Yuba County Water Agency and in consultation with the California Department of Fish and Game (DFG), National Marine Fisheries Service (NMFS), and U.S. Fish and Wildlife Service (USFWS), developed the Lower Yuba River Redd Dewatering and Fry Stranding Monitoring and Evaluation Plan (Jones & Stokes 2003). The following summarizes the history of study plan development and permitting to date: Phase 1 (aerial photography and habitat mapping) of the study was completed in Phase 2 (fish stranding surveys) was delayed because of the need to obtain federal and state research permits for take of juvenile steelhead and springrun Chinook salmon. A federal take permit (ESA Section 10) application was submitted to NMFS in April Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 2 April 2009 J&S

11 Yuba County Water Agency J&S attended three coordination meetings with DFG, USFWS, and NMFS between August and November 2005 to review the Phase 1 results and finalize the Phase 2 study plan. NMFS issued a Federal Register notice on January 24, 2006 announcing that the federal permit application was available for public review. On January 27, 2006, J&S prepared and submitted a California ESA take permit (Fish and Game Code 2081) application to DFG for take of spring-run Chinook salmon on January 27, J&S attended three meetings with the Yuba River Management Team between January and March 2006 to discuss the draft 2081 permit application and resolve issues related to the appropriate permitting mechanism, take estimation methods, and take minimization measures. The final 2081 application was submitted to DFG on March 22, In March 2006, NMFS concluded that federal take authorization for the fish stranding study was unnecessary because of existing coverage under the federal biological opinion for the Yuba River Development Project License Amendment. On September 11, 2006, DFG issued a Memorandum of Understanding to J&S authorizing take of spring-run Chinook salmon as described in the 2081 application. Objectives The primary objective of the study is to evaluate the effectiveness of FERC flow reduction and fluctuation criteria in minimizing dewatering and stranding of Chinook salmon and steelhead redds and fry in the lower Yuba River. In addition, in accordance with NMFS s Biological Opinion for the YRDP License Amendment (National Marine Fisheries Service 2005), the results of the study will serve as the basis for development and implementation of a flow reduction and fluctuation management plan that will identify additional actions, as needed, to minimize take of listed spring-run Chinook salmon and steelhead. Approach The proposed approach involves integration of key hydrologic variables, life history attributes, flow-habitat relationships, and habitat-survival relationships to evaluate the potential frequency and magnitude of biological effects associated with controlled flow reductions. The general components and analytical steps of the assessment are summarized below. 1. Describe the hydrologic and operating conditions affecting the frequency, seasonal timing, and magnitude of flow fluctuations and reductions in the lower Yuba River Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 3 April 2009 J&S

12 Yuba County Water Agency 2. Describe the key life history attributes affecting the seasonal timing, relative abundance, and sensitivity of Chinook salmon and steelhead to flow fluctuations and reductions 3. Identify the seasons or months of overlap between potential flow fluctuations and reductions (subject to the FERC flow fluctuation and reduction criteria) and Chinook salmon and steelhead incubation and fry rearing periods 4. Develop flow-habitat relationships to translate hydrologic characteristics of the flow fluctuations/reductions into habitat effects (e.g., reductions in water depths over redds) 5. Translate habitat effects into potential biological effects based on field observations and/or literature-based relationships between habitat conditions and fish survival or abundance 6. Evaluate long-term redd dewatering and fry stranding impacts based on the projected frequencies, seasonality, and magnitude of flow reductions (subject to the FERC flow fluctuation and reduction criteria) that would be expected in response to annual variability in hydrologic conditions The potential magnitude of redd dewatering and fry stranding varies seasonally and annually depending on natural variability in hydrologic conditions, project operating objectives, and resultant effects on the frequency, timing, and magnitude of flow reductions in the lower Yuba River. Therefore, the following report includes a description of the Yuba River Project and an assessment of the probable frequency, timing, and magnitude of controlled and uncontrolled flows based on current operating objectives and 20 years of hydrologic data. The potential magnitude of redd dewatering and fry stranding also depends on the seasonal timing of spawning, incubation, and fry rearing, and variation in abundance, developmental stage, and size of eggs, alevins, and fry relative to the timing of controlled flow reductions. Therefore, the general timing and relative abundance of Chinook salmon and steelhead/rainbow trout spawning, incubation, and fry rearing life stages are described in this report. Figure 1 illustrates the conceptual model and analytical approach for evaluating redd dewatering impacts associated with controlled flow reductions. The redd dewatering assessment will involve integration of hydrologic and life history information, stage-discharge relationships, habitat use data (redd depth distributions), and general assumptions regarding the relationship between water depth and the suitability of intergravel conditions for incubation and fry emergence. Figures 2 and 3 illustrate the conceptual model and analytical approach for evaluating fry stranding impacts (beaching and isolation) associated with controlled flow reductions. The fry stranding assessment will involve integration of hydrologic and life history information, and field evaluations designed to estimate the occurrence and extent of fish stranding for a number of representative flow reductions. In addition, the fry stranding assessment will also examine the potential effects of physical habitat conditions (bar slope, type and Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 4 April 2009 J&S

13 REDD DEWATERING Life History Timing of spawning and incubation (changes in relative abundance of eggs/alevins over time) Hydrology/Operations Frequency, timing, and magnitude of flow reductions during incubation season Frequency distribution of water depths selected by adults for spawning (redd depth distributions) Habitat Relationships Stage-discharge relationships in known spawning areas (changes in water depth as a function of flow) Habitat Effects Timing and magnitude of reductions in water depths in spawning areas Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Changes in frequency distribution of redd depths (water surface to top of tailspill) resulting from flow reduction Changes in frequency distribution of egg/alevin depths (water surface to depth of egg pocket reulting from flow reductioin) Biological Effects Proportion of redds and eggs/alevins potentially affected by flow reductions (mortality from reductions in water depth and intergravel flow) Conceptual model and analytical approach for evaluating potential redd dewatering impacts associated with implementation of the the flow fluctuation and reduction criteria Figure 1 Redd Dewatering

14 FRY STRANDING (BEACHING) Life History Timing of fry emergence and rearing (changes in relative abundance of fry over time) Hydrology/Operations Frequency, timing, magnitude, and rate of flow reductions during fry rearing season Relative abundance/densities of fry in shallow, nearshore areas on low-gradient bars Growth rates and changes in size of fry over time Habitat Relationships Stage-discharge relationships on low-gradient bars (rate of change in stage as a function of flow) Area-discharge relationships on low-gradient bars (amount of bar area exposed as a function of flow) Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Habitat Effects Timing, rate of change in stage, and amount of bar area exposed by flow reduction Biological Effects Presence/absence and relative abundance of beached fry on gravel bars Conceptual model and analytical approach for evaluating potential fry stranding (beaching) impacts associated with implementation of the flow fluctuation and reduction criteria. Figure 2 Fry Stranding (Beaching)

15 FRY STRANDING (ISOLATION) Life History Timing of fry emergence and rearing (changes in relative abundance of fry over time) Hydrology/Operations Frequency, timing, magnitude, and duration of flows during fry rearing season Distribution and abundance of fry in off-channel habitats Growth rates and changes in size of fry over time Habitat Relationships Type, number, location, and size of off-channel habitats disconnected from main river by flow reductions Habitat Effects Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Timing, duration, and area of connected and disconnected off-channel habitats Changes in habitat quantity/quality as a result of connection or disconnection Biological Effects Distribution and relative abundance of fry in disconnected off-channel habitats Mortality from dessication, thermal stress, predation, and food limitation Conceptual model and analytical approach for evaluating potential fry stranding (isolation) impacts associated with implementation of the flow fluctuation and reduction criteria. Figure 3 Fry Stranding (Isolation)

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17 Yuba County Water Agency size of off-channel habitats) in determining the relative magnitude of fry stranding. Study Tasks The following table summarizes the study tasks, progress to date, and data sources for each task. Table 1. Status of Study Tasks Task Products Data Source Task 1-1. Redd Surveys Field measurements of Chinook salmon and steelhead/rainbow trout redd depths USFWS Task 1-2. Life History Characterization (Eggs and Alevins) Task 2-1. Aerial Photography and Habitat Mapping Task 2-2. Habitat-Flow Relationships Task 2-3. Life History Characterization (Fry Rearing) Task 2-4. Fry Stranding Surveys Graphs of seasonal timing and relative abundance of Chinook salmon and steelhead eggs/alevins Aerial photography and digital shoreline maps of river and offchannel areas Relationships between flow and off-channel locations, surface areas, and connectivity at flows ranging from 700 to 4,300 cfs Graphs of seasonal timing and relative abundance of Chinook salmon and steelhead fry Results of bar and off-channel stranding evaluations for three flow reductions in April 2007, June 2007, June 2008 Results of long-term monitoring of selected off-channel habitats from June through December 2008 Updated GIS database of bar and off-channel study sites Chinook salmon carcass surveys, general life history information, embryo/alevin developmental rates (J&S ; DFG 2005, 2006) Aerial photographs of Yuba River at flows ranging from 700 to 4,300 cfs ( ) GIS database of aerial photographs and digital shoreline maps (2004) Chinook salmon carcass surveys, life history information, scientific literature (egg/alevin developmental rates), field monitoring programs and studies Bar stranding and off-channel survey data GPS data of bar and off-channel study sites Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 5 April 2009 J&S

18 Yuba County Water Agency Yuba Project Area and Facilities The Yuba Project Area encompasses storage and hydropower facilities of the Yuba Project, the Corps of Engineers, and PG&E, the Yuba River downstream from New Bullards Bar Reservoir, and the lower Yuba River downstream from Englebright Reservoir to the confluence with the Feather River. The Yuba Project Area is part of the larger Yuba River Basin that drains approximately 1,339 square miles of the western slope of the Sierra Nevada Mountains, including portions of Sierra, Placer, Yuba, and Nevada counties. The Yuba River is a tributary of the Feather River, which in turn is a tributary of the Sacramento River. The basin rises from an elevation of about 88 feet to about 8,590 feet above mean sea level (msl). The annual unimpaired flow at the Smartville Gage on the lower Yuba River has ranged from a high of 4.93 MAF in 1982 to a low of 0.37 MAF in 1977, with an average of about 2.37 MAF per year (1901 to 2005). In general, runoff is nearly equally divided between runoff from rainfall during October through March and runoff from snowmelt during April through September. The upper basins of the Middle Yuba and South Yuba rivers have been extensively developed for hydroelectric power generation and consumptive uses by Nevada Irrigation District (NID) and PG&E. Total storage capacity of about 307 TAF on the Middle Yuba and South Yuba rivers and associated diversion facilities enable both NID and PG&E to export an average of approximately 410 TAF per year from the Yuba River Basin to the Bear River and American River basins. In addition, the South Feather Water and Power Agency exports an average of about 70 TAF per year from Slate Creek (a tributary to the North Yuba River) to the Feather River Basin. While these upper basins lie outside of the project study area, the described operations can significantly reduce the water supply available to the lower Yuba River, particularly during dry and critical water years. The Corps and YCWA own storage facilities, and YCWA and PG&E own generating facilities, in the Yuba Project Area. Englebright Dam and Daguerre Point Dam were originally constructed by the California Debris Commission, for debris control and now are operated and maintained by the Corps. PG&E s Narrows I powerhouse is located downstream of Englebright Dam. The Yuba Project, constructed and operated by YCWA, is a multiple-use project that provides flood control, power generation, irrigation, recreation, and protection and enhancement of fish and wildlife. It includes New Bullards Bar Reservoir, New Colgate Powerhouse, and Narrows II Powerhouse. Englebright Dam and Reservoir and Daguerre Point Dam are not parts of the Yuba Project. However, Englebright Dam and Reservoir are used to regulate power peaking releases from the New Colgate Powerhouse, and Daguerre Point Dam is used by YCWA to divert water to its Member Units. The elements of the Yuba Project are described in more detail in the following subsections. Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 6 April 2009 J&S

19 Yuba County Water Agency New Bullards Bar Reservoir New Bullards Bar Reservoir, located on the North Yuba River, is the principal storage facility of the Yuba Project. The reservoir has a total storage capacity of 966 TAF with a minimum pool of 234 TAF (as required by YCWA s FERC license), thus leaving 732 TAF of capacity that can be regulated. A portion of this regulated capacity, 170 TAF, normally must be held empty from September through April for flood control. The North Yuba River inflow to New Bullards Bar Reservoir is augmented by diversions from the Middle Yuba River to Oregon Creek through the Lohmann Ridge Tunnel, and by diversions from Oregon Creek into the reservoir through the Camptonville Tunnel. The average total inflow to New Bullards Bar Reservoir from the North Yuba River and diversions from the Middle Yuba River and Oregon Creek is about 1.2 MAF per year. Releases from New Bullards Bar Reservoir are made through the New Colgate Powerhouse, which has a capacity of 3,700 cfs, or through the dam s bottom outlet, or gated spillway. Englebright Reservoir Englebright Dam and Reservoir were constructed in 1941 to capture sediment produced by upstream hydraulic mining activities. The reservoir is situated downstream of New Bullards Bar Dam, at the confluence of the Middle and South Yuba rivers. The average annual inflow to Englebright Reservoir, excluding releases from New Bullards Bar Reservoir, is approximately 400 TAF. Englebright Reservoir has a total storage capacity of approximately 70 TAF, but provides limited conservation storage because the reservoir is used to attenuate power peaking releases from New Colgate Powerhouse. Englebright Reservoir is used extensively for recreation. Englebright Dam has no low-level outlet. Water from Englebright Reservoir is released for power generation at the Narrows I and Narrows II powerhouses, or spilled over the top of the dam. Narrows I Powerhouse, owned by PG&E, is a 12 MW facility, with a discharge capacity of approximately 730 cfs and a bypass flow capacity (when the generator is not operating) of 540 cfs. Narrows II, which is part of the Yuba Project, is a 50 MW facility, with a discharge capacity of approximately 3,400 cfs and a bypass flow capacity of 3,000 cfs. YCWA and PG&E coordinate the operations of Narrows I and II for hydropower efficiency and to maintain relatively constant flows in the lower Yuba River. The Narrows I Powerhouse typically is used for low-flow reservoir releases (less than 730 cfs), or to supplement the Narrows II Powerhouse capacity during high flow reservoir releases. Annual maintenance requires the Narrows II Powerhouse to be shut down for a two- to three-week period, or longer if major maintenance is performed. Maintenance is typically scheduled for the beginning of September, or during the winter months. Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 7 April 2009 J&S

20 Yuba County Water Agency Under existing water rights and agreements, PG&E may release up to 45 TAF from Englebright Reservoir storage, although only about 10 TAF of storage normally are used. Fluctuations in Englebright Reservoir storage principally occur for daily or weekly regulation of winter inflows and New Colgate Powerhouse releases. Because of the recreational and power generation needs, the storage level within the reservoir seldom drops below 50 TAF. Lower Yuba River The lower Yuba River refers to the 24-mile section of the river between Englebright Dam and the confluence with the Feather River southwest of Marysville. Instream flow requirements are specified for the lower Yuba River at the Smartville Gage (RM 23.6), located approximately 2,000 feet downstream from Englebright Dam, and at the Marysville Gage (RM 6.2). Below the Smartville Gage, accretions, local inflow, and runoff contribute, on average, approximately 200 TAF per year to the lower Yuba River. Deer Creek flows into the Yuba River at approximately RM Dry Creek flows into the Yuba River at RM 13.6, approximately two miles upstream of Daguerre Point Dam. The flow in Dry Creek is regulated by BVID s operation of Merle Collins Reservoir, located on Dry Creek about 8 miles upstream from its confluence with the Yuba River. In recent years, irrigation diversions from the lower Yuba River at Daguerre Point Dam and upstream at BVID s Pumpline diversion facility have totaled approximately 300 TAF per year. Controlled release from New Bullards Bar reservoir may be made through the New Colgate powerhouse up to about 3500 cfs, and from the spillway gates at New Bullards Bar reservoir up to 50,000 cfs or more. Controlled releases from Englebright reservoir are made through the Narrows I and Narrows II powerhouse up to about 4200 cfs; above that releases are via the spillway at the top of Englebright dam and are essentially uncontrolled. Operations Objectives YCWA s Yuba Project has multiple operations objectives, including flood protection, releases for consumptive demands and power generation, and releases for environmental protection. The Corps Englebright Dam and Reservoir, and PG&E s Narrows I powerhouse are usually operated in coordination with the larger Yuba Project. Operations of Yuba Project can be described in terms of (1) water management operations (i.e., base flow operations), (2) storm runoff operations, and (3) flood control operations. Figure 4 provides a general overview of the operations objectives at different times of the year. As a result of these objectives, average lower Yuba River flows are consistently within a relatively narrow band (Figure 5). Under controlled conditions, typical flows in the Lower Yuba River would include minimum instream flows plus an operational buffer plus releases for consumptive (irrigation) demands. In wetter years, additional water is released to Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 8 April 2009 J&S

21 S/M S/FR S/FR S S S SI SI SI SI SI S/M October November December January February March April May June July August September LEGEND Base Flow/Water Management Operations - Typical Goal for Month S Spawning Flows - Consistent Flows when possible M Maintenance Flows FR Fall Rice - Irrigation releases for rice decomposition & duck habitat water SI Summer Irrigation - Irrigation releases to correspond to growing season (02-08) Figure 4 Seasonal Operations Objectives of the Yuba Project

22 % - 20% Exceedence Flow Range Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Smartville Flows Marysville Flows Figure 5 Average Monthly Flows (cfs) Lower Yuba River at Smartville and Marysville Gages

23 Yuba County Water Agency achieve target reservoir storage levels by the end of October, when flood pool requirements take effect. Base Flow Operations Base flow operations describe normal reservoir operations when system flows are controlled through storage regulation. These operations occur outside periods of flood control operations, spilling, bypassing uncontrolled flows into Englebright Reservoir, or high, unregulated inflows from tributary streams downstream from Englebright Dam. During base flow operations, releases are made for instream flows, consumptive deliveries, and power generation. Starting approximately September 1, releases will be set at the rates necessary to meet the controlling instream-flow requirement, which is at either the Marysville Gage or the Smartville Gage, plus any additional amount that is required for diversions. Diversions include fall base irrigation diversions and diversions for fall rice decomposition/duck water field flooding. Fall rice decomposition/duck field flooding typically starts in late September to early October and goes through mid November, and includes a ramp up to a maximum diversion rate of between 450 to 550 cfs. Diversions then ramp down during November and December as field flooding requirements decrease. After the completion of fall field flooding, releases under Base Flow/Water Management Operations drop down to the amounts necessary to meet the controlling minimum instream flow requirement. During approximately January through March, there normally are minimal diversions at Daguerre Point Dam, and Base Flow/Water Management Operations are set to maintain the releases necessary to meet the controlling instream flow requirement. Starting about April 1, Base Flow/Water Management Operations are conducted to meet multiple objectives, including a) meeting controlling minimum instream flow requirements, b) supplying sufficient water to meet water-supply contract requirements, c) meet the requirements of the Power Purchase Contract (PPC), and d) meet a September 30 New Bullards Bar Reservoir storage target of 650,000 acre-feet. Base Flow/Water Management Operations will be subject to the flow-fluctuation and ramping criteria in YCWA s pending application for FERC license amendment. Storm Runoff Operations Storm runoff operations occur during the storm season, typically between October and May. Storm runoff operations target Englebright Reservoir operations, because it is the downstream control point for releasing water into the Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 9 April 2009 J&S

24 Yuba County Water Agency lower Yuba River. Storm runoff operations guidelines for Englebright Reservoir specify target storage levels and release rates. During storm runoff operations, additional releases above releases for instream flows and consumptive deliveries are typically made to maintain control of reservoir levels in response to storm inflows. Specific Storm Runoff Operations decisions are highly dependent on the following factors: Amount and elevations of snowpack Storm forecasted precipitation and snow level Future storm forecasts PG&E generation schedule Time of year (New Bullards Bar Reservoir water storage flood-control requirements) Specific Storm Runoff Operations guidelines for Englebright Reservoir include holding the reservoir at a target level for as long as possible by varying releases through the Narrows I and II powerhouses. If storm flows into Englebright reservoir are high enough and the reservoir targets cannot be maintained, Englebright reservoir will spill. When storm flows into Englebright reservoir subside, flows below the reservoir are returned to the base flow levels in a controlled fashion. It should be noted that Storm Runoff Operations are not subject to the flowfluctuation and ramping criteria in YCWA s FERC license. Flood Control Operations During flood control operations, the seasonal flood pool specified in the Corps flood operation manual for New Bullards Bar Reservoir is kept evacuated for flood protection, and to avoid unnecessary flood control releases. Reservoir releases may be required to maintain flood control space between September 15 and June 1. During flood control operations, maintenance of reservoir storage targets and controlling river flows within safe parameters are paramount. When Flood Control Operations are in effect, Yuba Project reservoir operations are generally dictated by the Corps flood operations criteria or the Flood Control Joint Operations Center operated by DWR and the Corps. Flood operations are designed to protect life, property, and the dams from actual and anticipated major flood events. At the end of Flood Control Operations, flows shall be returned to Storm Runoff Operations or Base Flow/Water Management Operations as soon as practicable. It should be noted that Flood Control Operations are not subject to the flowfluctuation and ramping criteria in YCWA s FERC license. Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 10 April 2009 J&S

25 Yuba County Water Agency Yuba Project Area Hydrology Yuba Project operations are largely governed by hydrologic conditions. During dryer year classes, the Yuba Project may be operated to meet Base Flow operations objectives for much, or even all of the year. However, during wet year classes, the Yuba Project may be operated in response to storm runoff conditions, or in flood control mode, for several months of the year. The hydrology and operational requirements of the Yuba Project are relevant to the timing, frequency, and magnitude of flow changes in the Yuba that could lead to redd dewatering and or fry stranding. Also, the typical operational range of the Lower Yuba River, when operating under controlled conditions, provides some indication of the ranges of flow variation likely to be most common in the river. Figures 6 and 7 provide an indication of the typical range of flows in the Lower Yuba River by month. Figure 6 charts a time series of actual flows in the Lower Yuba, showing the 80%, median and 20% probability flows and the Accord flow Schedule 1 required flows at Marysville. Figure 7 provides the ranges of required flows in the Lower Yuba, including the upper (Schedule 1) and lower (Schedule 6) minimum instream flow requirements, plus the anticipated additional release to meet consumptive irrigation needs. In dryer conditions, the lower river is more likely to be operated in fairly close accordance with the required flows. In wetter year conditions, flows in addition to those shown are often necessary to ensure that the New Bullards Bar reservoir is sufficiently evacuated by October 1 to meet wintertime flood storage objectives. Hydrologic conditions on the Lower Yuba River can also be described in terms of exceedance curves. Figures 8 and 9 provide exceedance curves for the months of October and March. Flows that exceed 4,200 cfs are essentially uncontrolled in the Lower Yuba. The exceedance flows for the Lower Yuba River may be considered in terms of how often the Lower Yuba is in control, with flows below 4,200 cfs that may be actively adjusted up and down to meet the seasonal operations objectives. Any month of the year may be in control for the entire month; however, during some months the Lower River may never be in control. Figure 10 shows the potential for control of the Lower Yuba by month, including the range of potential flow control duration. On average, the months of December through June are not under control for some portion of the month, and the months of January through June have the potential to remain out of control for the entire month. To further relate Lower Yuba River control to the potential for flow fluctuations that may impact redds or fry, Figures 11 and 12 depict the Lower Yuba River stage for 2001 (a relatively dry year), and 2006 (a relatively wet year). Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 11 April 2009 J&S

26 Yuba County Water Agency Chinook Salmon and Steelhead Life History The following life history descriptions are based on information obtained from past and ongoing fish monitoring programs and studies in the lower Yuba River, field observations during 2007 fry stranding surveys, and general predictions of life stage occurrence based on developmental and growth rates of Chinook salmon and steelhead reported in the literature. Chinook Salmon Figure 13 depicts the general timing and relative abundance of Chinook salmon spawning, incubation, and juvenile life stages in the lower Yuba River. Annual carcass surveys since 1994 indicate that Chinook spawning begins in September, peaks in late October or early November, and declines to low levels by the end of December. Small numbers of spawning salmon have been reported through March. Based on water temperatures that typically range from 46 F to 59 F during the incubation period, fry emergence would be expected to occur from November through May with most fry emerging from the gravel from December through March. Chinook salmon fry less than 50 millimeters (mm) in length generally peak in abundance from January through March but may continue to present through May. By the end of May, most juveniles are greater than 50 mm in length and have begun their seaward migration. Steelhead Figure 14 depicts the general timing and relative abundance of steelhead spawning, incubation, and juvenile rearing life stages in the lower Yuba River. In recent years, most spawning adults and redds have been observed in the Yuba River from January through May, but redds have been observed as late as August. Many of the late spawning fish appear to be resident rainbow trout based on their body size. Assuming 7 to 9 weeks for incubation, fry emergence would be expected to occur primarily from March through July. Steelhead/rainbow trout fry less than 50 mm in length typically peak in abundance from May through July but may continue to be present through September. By October, most juveniles are greater than 50 mm in length. These fish overwinter and spend a minimum of one year in freshwater before migrating to the ocean. Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 12 April 2009 J&S

27 Range of Flow, Marysville 20% Exceedance, Median, 80% Exceedance Flow, CFS Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 80% Median 20% Sched 1 Range of Flow, Marysville 10% Exceedance, Median, 90% Exceedance Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Flow, CFS Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 90% Median 10% Sched 1 Figure 6 Typical Range of Flows and Probability of Exceedance in Lower Yuba River by Month

28 3,500 3,000 2,500 Flow (cfs) 2,000 1,500 1,000 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS /1 10/15 10/29 11/12 11/26 12/10 12/24 1/7 1/21 2/4 2/18 3/4 3/18 4/1 Upper Flow Range at Smartville Lower Flow Range at Smartville Upper Flow Range at Marysville Lower Flow Range at Marysville 4/15 4/29 5/13 5/27 6/10 6/24 Figure 7 Typical Range of Anticipated Yuba River Flows Under the Yuba River Accord 7/8 7/22 8/5 8/19 9/2 9/16 9/30

29 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Flow (cfs) 4,200 4,000 3,800 3,600 3,400 3,200 3,000 2,800 2,600 2,400 2,200 2,000 1,800 1,600 1,400 1,200 1, % 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Exceedance Probability Yuba River Flow at Marysville Yuba River Flow at Smartville Unimpaired Flow at Smartville Figure 8 Exceedance Probability of Historical Mean Daily Yuba River Flows in October ( )

30 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Flow (cfs) 4,200 4,000 3,800 3,600 3,400 3,200 3,000 2,800 2,600 2,400 2,200 2,000 1,800 1,600 1,400 1,200 1, % 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Exceedance Probability Yuba River Flow at Marysville Yuba River Flow at Smartville Unimpaired Flow at Smartville Figure 9 Exceedance Probability of Historical Mean Daily Yuba River Flows in March ( )

31 100 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS % of TIme River Under Control Wettest Years: May have no control Jan - June, Partial control Dec & Jul Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep % of Time in Control (Flow < 4200 CFS) Figure 10 Likelihood of Controlled Flows (Percent of Time Flows were Less Than 4,200 cfs at Smartville Gage, )

32 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Stage (ft) 9.2 4, , , , , , , , , , , , , , , , , /1/00 10/15/00 10/29/00 11/12/00 11/26/00 12/10/00 12/24/00 1/7/01 1/21/01 2/4/01 2/18/01 3/4/01 3/18/01 4/1/01 4/15/01 4/29/01 5/13/01 5/27/01 6/10/01 6/24/01 7/8/01 7/22/01 8/5/01 8/19/01 9/2/01 9/16/01 9/30/01 Yuba River Stage at Smartville Yuba River Stage at Marysville Yuba River Flow at Smartville Yuba River Flow At Marysville Flow (cfs) Figure 11 Historical Daily Average Yuba River Stage at Smartville and Marysville (WY 2001)

33 Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Stage (ft) /1/05 10/15/05 10/29/05 11/12/05 11/26/05 12/10/05 12/24/05 1/7/06 1/21/06 2/4/06 2/18/06 3/4/06 3/18/06 4/1/06 4/15/06 Yuba River Stage at Smartville Yuba River Stage at Marysville Yuba River Flow at Smartville Yuba River Flow At Marysville 4/29/06 5/13/06 5/27/06 6/10/06 6/24/06 7/8/06 7/22/06 8/5/06 8/19/06 9/2/06 9/16/06 9/30/06 4,200 4,000 3,800 3,600 3,400 3,200 3,000 2,800 2,600 2,400 2,200 2,000 1,800 1,600 1,400 1,200 1, Figure 12 Historical Daily Average Yuba River Stage at Smartville and Marysville (WY 2006) Flow (cfs)

34 Chinook Salmon Spawning 100 Relative Abundance Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul 100 Chinook Salmon Eggs/Alevins Relative Abundance Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Relative Abundance Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Chinook Salmon Fry (<50mm) Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Figure 13 General Timing and Relative Abundance of Chinook Salmon Spawning, Incubation, and Fry Rearing Life Stages

35 Steelhead Spawning 100 Relative Abundance Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct 100 Steelhead Eggs/Alevins Relative Abundance Graphics/Projects/ /Lower Yuba River Redd Watering and Fry Strnading 2008 Annual Report (03-09) SS Relative Abundance Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Steelhead Fry (<50mm) Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Figure 14 General Timing and Relative Abundance of Steelhead Spawning, Incubation, and Fry Rearing Life Stages

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37 Yuba County Water Agency Habitat Mapping Aerial photographs of the lower Yuba River were taken in August 2002, February 2003, and May 2003: Table 2. Dates of Aerial Photographs and Mean Daily Flows Flight Date Flow at Smartville Gage (cfs) Flow at Marysville Gage (cfs) August 16, ,015 1,642 August 19, ,589 1,265 August 22, , August, 27, August 30, February 4, ,674 2,915 May 16, ,307 4,564 The photographs taken in 2002 were taken during controlled stepped reductions from 2,015 to 718 cfs (measured at the Smartville gage). Photographs were also taken on February 4 and May 16, 2003, to document the river at higher flows. All photographs were taken from a fixed-wing aircraft at 1:24,000 scale using Airborne GPS/Applanix Inertial Measuring Unit technology. Field-surveyed ground control and analytical aerotriangulation techniques were used to determine ground coordinates of each photographic series and to ensure accurate mapping of spatial features. A digital orthophotograph of the lower Yuba River was created from the color photographs taken on August 30, The photograph was spatially corrected using a digital terrain model of the lower Yuba River developed by the U.S. Army Corps of Engineers and YCWA. Digital photogrammetric techniques were used to delineate the shoreline (water s edge) of the main river, side channels, backwaters, and other discernable surface-water features at each documented flow. The digital shoreline maps were compiled and stored as AutoCAD files. The orthophotograph and digital shoreline maps were imported into a GIS database and used to map the location and size of off-channel habitats and the presence or absence of a surface connection with the main river at different flows. This database will serve as a mapping and analytical tool that will be expanded and updated as field surveys are conducted and new information is developed on the relationship between fish stranding and flow fluctuations during the course of the study. Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 13 April 2009 J&S

38 Yuba County Water Agency 2008 Fish Stranding Surveys Methods Fish stranding surveys were conducted from May 29 through June 4, 2008, to evaluate bar and off-channel stranding associated with a scheduled flow reduction on June 1, On June 1, 2008, Narrows 2 releases were reduced from 1,400 to 1,150 cfs between the hours of 0100 and 0400 at a rate of approximately 100 cfs per hour (Figure 15). Periodic surveys and water temperature monitoring of several off-channel sites were conducted from June 30 through December 22 to monitor habitat conditions and abundance of juvenile Chinook salmon following the flow reduction on June 1, Bar Stranding A snorkeling survey was conducted in the Yuba River between Rose Bar and the State Route 20 bridge on May 29, 2008, to establish bar stranding study sites before the June 1 flow reduction. Underwater observations were focused on shallow (<6 inches deep), nearshore areas and low gradient bars (<5% slope) where the potential for bar stranding was considered highest. Three sites, each encompassing 100 meters (328 feet) of shoreline, were selected for the bar stranding evaluation. These sites were located adjacent to major riffles with relatively high densities of juvenile salmon and steelhead/rainbow trout in nearshore areas. In 2008, site 3 was reestablished at the same location used in Sites 1 and 2 were established at two new locations based on observed fish densities. On May 31, before the flow reduction, six transects were established at regular intervals (every 17 meters or 55 feet) along each 100-meter shoreline. Transects were 2 meters (6.6 feet) wide and extended perpendicular to the shoreline. A numbered flag was placed at the intersection of the shoreline and each transect to mark the points where intensive searches for fish would begin the following day. The dominant substrate sizes in each transect were noted. Water surface levels were measured at a fixed location at site 3. At dawn on June 1, field crews intensively searched the dewatered portion of each transect for stranded fish. The species, number, and lengths (10 mm size classes) of stranded fish were recorded. Field crews searched only areas that had no visible surface water or surface connections to the river. All transects were cleared of cobble, boulders, and other debris where fish potentially could hide. The length of each transect that was searched for fish was recorded and multiplied by 2 meters (6.6 feet) to determine the total search area. Handheld global positioning system (GPS) receivers (Trimble GeoXT with TerraSync software) were used to record the position of shorelines (before and Lower Yuba River Redd Dewatering and Fry Stranding Study 2008 Annual Report 14 April 2009 J&S