Lower Yuba River Redd Dewatering and Fry Stranding Monitoring and Evaluation Plan

Transcription

1 Lower Yuba River Redd Dewatering and Fry Stranding Monitoring and Evaluation Plan Prepared for: Yuba Count Water Agency 1402 D Street Marysville, CA Contact: Curt Aikens 530/ Prepared by: Jones & Stokes 2600 V Street Sacramento, CA Contact: Bill Mitchell 916/

2 Jones & Stokes Monitoring and Evaluation Plan. November. (.) Sacramento, CA.

3 Contents Page Monitoring and Evaluation Plan... 1 Introduction... 1 Objectives... 2 Flow Fluctuation Effects... 3 Redd Dewatering... 3 Fry Stranding... 4 Study Area... 6 Flow Evaluation Range... 7 Approach... 7 Task 1. Redd Dewatering Monitoring and Evaluation... 7 Task 2. Fry Stranding Monitoring and Evaluation... 8 Task 3. Reporting and Coordination... 9 Methods... 9 Task 1. Redd Dewatering Monitoring and Evaluation... 9 Task 2. Fry Stranding Monitoring and Evaluation Task 3. Reporting and Coordination Schedule References Cited Printed References Personal Communications Monitoring and Evaluation Plan i

4 Tables and Figures Table Follows Page 1 Proposed Schedule for 2004 Redd Dewatering and Fry Stranding Monitoring and Evaluation Activities Figures Follows Page 1 Lower Yuba River Steps Used to Compute Redd Dewatering Index for Specific Flow Reduction Steps Used to Compute Fry Stranding Index for Specific Flow Reductions Acronyms and Abbreviations cfs cubic feet per second cm/h centimeters per hour D-1644 State Water Resources Control Board Decision-1644 DFG California Department of Fish and Game GIS geographic information systems GPS global positioning system HSC habitat suitability criteria IFIM Instream Flow Incremental Methodology mm millimeters NOAA Fisheries National Oceanographic and Atmospheric Administration, National Marine Fisheries Service PG&E Pacific Gas and Electric Company PHABSIM Physical Habitat Simulation RM River Mile SWRCB State Water Resources Control Board USFWS U.S. Fish and Wildlife Service USGS U.S. Geological Survey YCWA Yuba County Water Agency Monitoring and Evaluation Plan ii

5 Lower Yuba River Redd Dewatering and Fry Stranding Monitoring and Evaluation Plan Introduction On March 1, 2001, the State Water Resources Control Board (SWRCB) 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 fluctuation and reduction criteria (pages ) 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 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. Monitoring and Evaluation Plan 1

6 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. D-1644 also required the permittee to prepare and implement a redd dewatering and fry stranding monitoring and evaluation plan: By July 1, 2001, permittee shall submit for approval of the Chief of the Division of Water Rights a plan that describes the scope and duration of studies to be conducted to verify that salmon and steelhead redds and fry are being adequately protected from dewatering or stranding. Permittee shall consult with the Department of Fish and Game, the United States Fish and Wildlife Service, and the National Marine Fisheries Service regarding the development and scope of the plan. Following approval of the plan, the studies shall be conducted in accordance with the schedule specified in the plan. Pending completion of the studies, summary reports shall be submitted annually to the Division of Water Rights by December 31 and a final report with recommendations should be submitted within one year of the completion of the study. On June 29, 2001, Yuba County Water Agency (YCWA) transmitted the initial study plan to the SWRCB, the California Department of Fish and Game (DFG), the National Oceanographic and Atmospheric Administration, National Marine Fisheries Service (NOAA Fisheries), and U.S. Fish and Wildlife Service (USFWS). On November 9, 2001, following receipt of agency comments, the SWRCB requested that YCWA address these comments in a revised plan and to submit the plan by February 9, On January 23, 2002, YCWA submitted the revised plan to the SWRCB with a request to extend the deadline for submitting the final revised plan to allow sufficient time for agency review and comment. Following a meeting with the resource agencies and receipt of written comments, YCWA made further revisions and submitted the plan to the SWRCB on March 1, The March 2002 plan was approved by the SWRCB on April 17, Since then, the plan has been revised in response to additional comments received from the resource agencies during subsequent coordination meetings. Objectives In response to D-1644, YCWA proposes to conduct a 4-year program to monitor and evaluate the effects of flow fluctuations and reductions on redd dewatering and fry stranding in the lower Yuba River. The primary objective of the program will be to determine whether the D-1644 flow fluctuation and reduction criteria adequately protect Chinook salmon and steelhead redds and fry from dewatering or stranding. The specific objectives will be to: determine the potential magnitude of redd dewatering in relation to the timing and magnitude of flow fluctuations and reductions; Monitoring and Evaluation Plan 2

7 determine the potential magnitude of fry stranding in relation to the timing, magnitude, and rate of flow fluctuations and reductions; evaluate the effectiveness of the D-1644 flow fluctuation and reduction criteria in protecting redds and fry; and recommend additional measures to protect redds and fry from flow fluctuations and reductions, if warranted. In addition to modifications to the existing criteria, additional measures may include physical modifications of the channel to minimize impacts in areas where relatively high incidences of redd dewatering or fry stranding are detected. Flow Fluctuation Effects Redd Dewatering Redd dewatering can adversely affect salmonid eggs and alevins (pre-emergent fry) by impairing development and causing direct mortality as a result of desiccation, insufficient oxygen, and thermal stress (Neave 1953; McNeil 1966; Becker et al. 1982, 1983; Reiser and White 1981, 1983). Laboratory studies have shown that survival of salmonid eggs and alevins in dewatered redds depends on developmental stage, intragravel conditions, and the magnitude and duration of dewatering (Reiser and White 1983; Becker et al. 1982, 1983; Neitzel and Becker 1985; Bjornn and Reiser 1991). Chinook salmon and steelhead eggs and embryos can survive for several days to weeks in completely dewatered gravel, provided they remain moist and temperatures do not exceed tolerance limits. In contrast, newly hatched alevins are generally intolerant of dewatering, but may survive redd dewatering if exposure is brief and sufficient subsurface flow is present (Becker et al. 1982, 1983; Neitzel and Becker 1985). Flow reductions that reduce the depth and velocity of water over the redd can also have adverse effects if intragravel flows are reduced sufficiently to restrict the supply of oxygen to developing eggs and alevins. The sensitivity of Chinook salmon eggs to sustained low flows (little or no surface flow) is related to the amount of fine sediment in the redd, which acts to impede the flow of water through the redd (Reiser and White 1983, 1990). However, if flows drop below the level of the eggs, fine sediment in redds can improve survival by slowing the rate of drainage, retaining moisture, and restricting temperature changes (Becker et al. 1983). Becker and Neitzel (1985) cautioned that extrapolation of laboratory results to field situations is complicated by the high degree of variability in streams and the complex relationships between physical and biologic variables that affect survival of salmonid eggs and alevins under natural conditions. Site-specific factors that influence the effect of redd dewatering on eggs and alevins include residual flow (rate, duration, and proximity of intragravel flow), moisture retention, water temperature, gravel composition, dissolved oxygen, species characteristics (e.g., spawning-site selection), and alevin behavior (Becker and Neitzel 1985). Monitoring and Evaluation Plan 3

8 The D-1644 flow fluctuation criteria to protect Chinook salmon and steelhead redds (conditions d and e above) were based on field observations and the results of a redd dewatering analysis conducted by YCWA for the 1992 SWRCB hearing (Jones & Stokes 1992). Jones & Stokes developed quantitative relationships between flow reductions and potential impacts on Chinook salmon based on stage-discharge relationships developed by Beak Consultants (Beak Consultants 1989) for transects representing primary fall-run Chinook salmon spawning areas in the lower Yuba River. Potential impacts, expressed as the percentage of redds affected, were assessed for various combinations of initial spawning flows and subsequent flow reductions based on corresponding reductions in river stage (i.e., water surface elevation) and the frequency with which certain depths are used for spawning. Because the effects of flow fluctuations on eggs and alevins in the lower Yuba River had not been investigated, it was assumed that reductions in water depths to less than 2 inches above the streambed could adversely affect survival. Fry Stranding Juvenile salmonids and other aquatic organisms can become stranded on gravel bars or isolated in off-channel habitats (e.g., side channels, backwaters) as a result of flow fluctuations in rivers. Mortality of stranded salmonids and invertebrates can occur rapidly from exposure to air on gravel bars or within hours to days in potholes and other isolated waters as a result of thermal stress, oxygen depletion, and predation. Other potential causes of mortality include stress related to crowding and competition for food. Stranding has been reported to occur under both natural and controlled flow fluctuations, but significant stranding events have generally been associated with large, rapid flow reductions related to reservoir and hydropower operations (Hunter 1992). The incidence of stranding is related to several factors, including channel morphology, substrate type, species and life stage presence and abundance, time of year, river stage, and the magnitude, rate, and frequency of flow fluctuations. The vulnerability of fish to stranding is a function of their size and their behavioral response to changing flows, which depends on species, water temperature, time of year, and time of day. Newly emerged fry appear to be most vulnerable to stranding because of their limited swimming ability, their tendency to use the substrate as cover, and their preference for shallow river margins. As juveniles grow, they tend to move to deeper, higher-velocity water associated with main channel habitats where they are less susceptible to stranding. Field and laboratory observations indicate that juvenile salmonids are most susceptible to stranding when water temperatures drop below 4 8ºC (39 46ºF), because juveniles become relatively inactive and generally seek cover at these temperatures (Chapman and Bjornn 1969). For example, Bradford et al. (1995) found that relatively high proportions of juvenile coho salmon and rainbow trout were stranded on simulated gravel bars and pools when subjected to rapid flow reductions during the winter at temperatures of 3.5 4ºC (38 39ºF). Significantly more juvenile salmon and trout were stranded during the day than at night because they concealed themselves in the substrate during the day and left the Monitoring and Evaluation Plan 4

9 substrate at night. In similar experiments with juvenile Chinook salmon during spring, fry stranding rates were much lower than those observed for coho salmon and rainbow trout under winter conditions, although higher numbers of Chinook salmon fry were stranded on gravel bars at 6ºC (43ºF) than at 12ºC (54ºF) (Bradford 1997). In these experiments, the time of day had no significant effect on stranding rates. However, field observations suggest that Chinook salmon fry may be more susceptible to stranding during the day while steelhead fry may be more susceptible at night (Olson and Metzgar 1987, Hunter 1992). Bradford et al. (1995) and Bradford (1997) found that flow ramping rate affected the incidence of stranding. Under winter conditions, significantly more coho salmon and rainbow trout juveniles were stranded on simulated gravel bars and side channels at ramping rates of 30 centimeters per hour (cm/h) (11.8 inches per hour) than at 6 cm/h (2.4 inches per hour). Similar results were reported for juvenile Chinook salmon in simulated side channels during the fall (Bradford et al. 1995). Based on a field investigation of stranding of Chinook salmon and steelhead fry in the Sultan River, Washington, Olson and Metzgar (1987) recommended a schedule of variable ramping rates ranging from 1 to 6 inches per hour (2.5 to 15 cm/h) depending on flow range, season, and time of day. The slope of gravel bars can also affect the incidence of stranding. Stranding of chinook salmon and steelhead juveniles has been reported to increase on bars with slopes less than 4% (Hunter 1992, Bradford et al. 1995). A review of salmon stranding studies indicate that stranding on bars tends to occur on bars with <5% slope and that salmon fry are most vulnerable to stranding on bars with <2% slope (California Department of Fish and Game 2001). In recent years, YCWA has been conducting field surveys in the lower Yuba River to monitor the general distribution patterns of juvenile salmon and steelhead from year to year, and to assess the potential magnitude of stranding associated with scheduled flow reductions. The results of these ongoing surveys are being used by YCWA to manage operations and maintenance schedules to reduce potential stranding impacts. These surveys indicate that isolation of juvenile Chinook salmon in off-channel habitats occurs under both regulated and unregulated flow fluctuations, and that the magnitude of stranding appears to be a function of habitat quality as well as the period of time that juveniles have access to these habitats (Jones & Stokes 1999). While slow, gradual ramping rates are important in minimizing gravel bar stranding, isolation of juveniles in offchannel habitats may occur regardless of ramping rate because of favorable rearing conditions in these habitats, the distance of these habitats from the main river, and an apparent reluctance of juveniles to move away from protective cover (Bradford et al. 1995; Higgins and Bradford 1996; Bradford 1997; Jones & Stokes 1999). Factors that may influence fish survival in these off-channel habitats include the duration of reduced flows, water temperatures, food abundance, cover, and predator abundance. For example, young salmon have been sustained in large, isolated backwaters along the lower Yuba River where significant subsurface flows maintain suitable habitat through the spring and summer (Jones & Stokes 1998, 1999). Monitoring and Evaluation Plan 5

10 Study Area The lower Yuba River extends approximately 24 miles from Englebright Dam to its confluence with the Feather River near Marysville, California. Englebright Dam is the upstream limit of salmon and steelhead migration. The study area extends from the downstream end of the Narrows to the Yuba River s confluence with the Feather River (Figure 1). This area encompasses nearly all the Chinook salmon and steelhead spawning and rearing habitat in the lower Yuba River. Beak Consultants (1989) divided the lower Yuba River into four major study reaches: the Narrows, Garcia Gravel Pit, Daguerre Point Dam, and Simpson Lane reaches. The Narrows reach extends approximately 2 miles from Englebright Dam to the downstream end of the Narrows (River Mile [RM] 22). This reach is characterized by a relatively steep, bedrock-confined channel consisting of a series of rapids and deep pools. During controlled releases, water is discharged from Englebright Reservoir to the lower Yuba River through YCWA s Narrows 2 powerhouse and/or Pacific Gas and Electric Company s (PG&E s) Narrows 1 powerhouse, located immediately downstream of Englebright Dam. Deer Creek enters the Narrows reach approximately 0.7-mile downstream of Englebright Dam. The Narrows reach was not included in the study area because of the lack of significant spawning habitat or potential stranding areas. The Garcia Gravel Pit reach extends approximately 10.5 miles from the downstream end of the Narrows to Daguerre Point Dam (RM 11.5). This reach is characterized by a relatively wide, sinuous channel with alternating sequences of pools, runs, and riffles. The streambed and adjacent bars are composed predominantly of cobble and gravel. This reach supports 60-70% of the Chinook salmon spawning and all or most of the steelhead spawning in the lower Yuba River. Downstream of Long Bar (RM 14), the channel is confined by steep tailings of gravel and cobble from past gold mining operations. Dry Creek enters this reach approximately 3 miles upstream of Daguerre Point Dam. The Daguerre Point Dam reach extends approximately 8 miles from Daguerre Point Dam to RM 3.5 near Marysville. This reach is similar in character to the Garcia Gravel Pit reach but has a lower gradient and a higher proportion of pools. During the irrigation season (primarily April-August), flows in this reach are affected by diversions at Daguerre Point Dam. This reach supports 30-40% of the Chinook salmon spawning in the lower Yuba River. The Simpson Lane reach extends from RM 3.5 to the Feather River confluence (RM 0). This is reach is characterized by a low-gradient, levee-confined channel dominated by deep pools and fine-grained substrate (sand and gravel). Flows at various points in the river will be estimated based on hourly and daily flows measured at the nearest upstream gages located on the main river, tributaries, and diversion canals. Flows are continuously measured in the lower Yuba River at two locations: approximately 0.5-mile downstream of Englebright Dam (U.S. Geological Survey [USGS] Smartville gage) and at RM 7 near Monitoring and Evaluation Plan 6

11 Englebright Reservoir Narrows 1 and 2 Powerhouses and USGS Smartville Gage Creek Dry Long Bar The Narrows Deer Deer Creek Creek Daguerre Point Dam Parks Bar Narrows Reach Smartville Marysville Gage River Yuba Goldfields Garcia Gravel Pit Reach Yuba Daguerre Point Dam Reach Marysville Simpson Lane Reach miles Jones & Stokes Figure 1 Lower Yuba River

12 Marysville (USGS Marysville gage). Tributary inflows and diversion flows are measured daily at gages on Deer Creek, Dry Creek, and the irrigation canals near Daguerre Point Dam. Flow Evaluation Range Redd dewatering and fry stranding will be evaluated over a range of flows defined by the current instream flow requirements, the operating range of the Narrows 1 and Narrows 2 powerhouses, and the D-1644 flow fluctuation and reduction criteria (400 4,000 cubic feet per second [cfs], measured at the Smartville gage). Under the D-1644 criteria, various possible flow fluctuations and reductions could occur within the flow evaluation range. Monitoring and evaluation of fry stranding will include field surveys to document the occurrence and relative magnitude of stranding associated with a range of representative flow reductions within the flow evaluation range. The ability to create these flow conditions or control their timing will be subject to hydrological, operational, and regulatory constraints. Therefore, planning will be conducted with the project operators on an ongoing basis to identify opportunities to achieve a range of representative flow conditions. Potential opportunities include flow changes associated with normal operations, maintenance activities, and water transfers. In addition, opportunities will be identified to manipulate flows specifically for the purpose of testing conditions that would not otherwise occur under normal operations (e.g., hourly ramping rates from 100 to 500 cfs). To minimize potential bar stranding impacts, the slowest ramping rate will be tested first and then progressively increased until bar stranding is observed or the fastest ramping rate is reached. Larger reductions or ramping rates may occur from flood-control operations, bypasses of uncontrolled Englebright inflows, emergencies, uncontrolled spills, or tributary inflows downstream of Englebright Dam. Such changes are not subject to the D-1644 flow fluctuation and reduction criteria. Approach Task 1. Redd Dewatering Monitoring and Evaluation The effectiveness of the D-1644 flow fluctuation and reduction criteria in protecting Chinook salmon and steelhead redds will be evaluated using a combination of habitat modeling results and information on the timing and distribution of spawning in the lower Yuba River. The USFWS is currently conducting a study on the lower Yuba River to identify potential instream flow requirements for Chinook salmon and steelhead (U.S. Fish and Wildlife Service 2002). The study includes the development of habitat suitability criteria (HSC) and the use of a 2-dimensional hydraulic model to predict changes in the quantity and quality of spawning and rearing habitat as a function of flow (Harlow pers. comm.). Potential redd dewatering impacts will be evaluated using a habitat modeling method ( effective habitat analysis ) that quantifies the effect of flow reductions on the amount of suitable habitat for hatching and fry emergence Monitoring and Evaluation Plan 7

13 (incubation habitat) based on changes in water depths and velocities in potential spawning areas. The results of this analysis will be used in combination with information on the timing and distribution of spawning to develop relationships between flow reductions and the potential magnitude of redd dewatering. Jones & Stokes will continue to work with the USFWS to identify common data needs and opportunities to coordinate efforts to achieve the objectives of both studies. Thus far, coordination activities have included the development of a common photographic base map for habitat mapping, exchanges of field data, and planning efforts to collect HSC data for steelhead spawning in Redd dewatering monitoring and evaluation will be divided into the following tasks: 1-1. Conduct field surveys to map the location of steelhead redds and measure water depths, velocities, and substrate size at these redds for HSC development Describe the timing and distribution of fall-run Chinook salmon, spring-run Chinook salmon, and steelhead spawning in the lower Yuba River Evaluate potential redd dewatering impacts associated with the D-1644 flow fluctuation and reduction criteria based on the results of Task 1-2 and the USFWS s effective habitat analysis. Task 2. Fry Stranding Monitoring and Evaluation The effectiveness of the D-1644 flow fluctuation and reduction criteria in protecting Chinook salmon and steelhead fry will be evaluated using a combination of habitat mapping, field surveys, and information on the timing and distribution of fry rearing in the lower Yuba River. Aerial photographs and digital shoreline maps of the river at the selected flows will be used to identify potential stranding sites (e.g., side channels, backwaters, low-gradient bars) and to determine the distribution, extent, and status (e.g., isolated or not isolated from the main river) of these sites as a function of flow. Field surveys would then be conducted to verify the status of potential stranding sites, document site characteristics, and determine the occurrence and extent of fry stranding or isolation. The results will be used in combination with information on the timing and distribution of fry rearing to develop relationships between the selected flow reductions and the potential magnitude of fry stranding. Fry stranding monitoring and evaluation will be divided into the following tasks: 2-1. Develop photographic base maps to identify and delineate potential fry stranding sites at various flows within the flow evaluation range Develop relationships between flow and the extent, distribution, and status of potential fry stranding sites. Monitoring and Evaluation Plan 8

14 2-3. Describe the timing and distribution of Chinook salmon and steelhead fry emergence and rearing in the lower Yuba River Conduct Chinook salmon and steelhead fry surveys to further characterize the status and physical conditions at potential stranding sites (e.g., connection with main river), and determine the presence and relative abundance of fry in these sites Evaluate potential fry stranding impacts for each of the selected flow reductions based on the results of Tasks 2-2, 2-3, and 2-4. Task 3. Reporting and Coordination Jones & Stokes will coordinate with YCWA, PG&E, DFG, NOAA Fisheries, and USFWS on an ongoing basis to discuss the monitoring results, identify flow evaluation opportunities, and develop specific strategies to achieve representative flow conditions. This includes periodic review and possible modification of the target flow conditions as new information is developed during the course of the program. Reports will be submitted to the SWRCB, DFG, NOAA Fisheries, and USFWS at the end of each program year, and a final report will be submitted following completion of the program. Methods Task 1. Redd Dewatering Monitoring and Evaluation Task 1-1. Redd Surveys The USFWS has been collecting habitat suitability data for Chinook salmon and steelhead spawning since November Thus far, the USFWS has collected sufficient data to develop HSC for fall- and spring-run Chinook salmon, and plans to continue surveys in 2003 to collect additional data for steelhead. Jones & Stokes and the USFWS will coordinate survey efforts to collect the additional data needed to develop spawning HSC for steelhead. Redd surveys will be conducted every 2 3 weeks during the primary steelhead spawning period (February April 2003). Surveys will extend from the downstream end of the Narrows (RM 22) to RM 3.5. Thus far, the USFWS has collected habitat suitability data for 47 steelhead redds. The goal will be to collect data on 103 additional redds to achieve the minimum recommended sample size (150 observations) for HSC development (Bovee 1986). Surveys will be conducted by boat and wading during periods when water clarity permits visual detection of redds. In deep areas where the streambed cannot be clearly seen from the surface, the USFWS proposes to use an underwater video system suspended from a boat to detect redds. During deep-water surveys, a series of parallel runs will be made in an upstream direction in selected habitats. Monitoring and Evaluation Plan 9

15 The locations of redds (shallow and deep) will be recorded with a global positioning system (GPS) unit. Habitat suitability data will be collected only for active redds (those not covered by periphyton growth). Where individual redds are indistinct because of high redd densities or superimposition, the approximate number of redds and degree of superimposition will be recorded. Steelhead redds will be distinguished from Chinook salmon redds based on length and width criteria developed for Chinook salmon and steelhead redds in the lower American River (U.S. Fish and Wildlife Service 2002). Water depths and velocities will be measured in areas adjacent to redds (or redd clusters) that are judged to have similar depths and velocities to those that were present at redd locations before redd construction. In addition, water depths will be measured at the shallowest portion of the tailspill. Water depths and velocities measured at individual redds will be considered valid only if fish are observed on redds or it can be reasonably assumed that redds were constructed at approximately the same flow present at the time of data collection. Water depths and mean column velocities will be measured with a top-setting rod equipped with a Marsh McBirney model 2000 or a Price AA velocity meter. In deep water, water depth and velocity will be measured over redds with an Acoustic Doppler Current Profiler. Depth will be recorded to the nearest 0.1 foot and velocity will be recorded to the nearest 0.01 foot per second. The dominant substrate size (particle size occupying the most area) will be visually assessed at three locations (the front of the pit, the sides of the pit, and the tailspill) using the following substrate coding system: Code Type Particle Size (inches) 0.1 Sand/silt <0.1 1 Small gravel Medium gravel Medium/large gravel Large gravel Gravel/cobble Small cobble Small cobble Medium cobble Large cobble Large cobble Boulder/bedrock >12 Source: U.S. Fish and Wildlife Service (2002) The length and width of each redd will be measured along the central axes of the pit and tailspill. In deep water, substrate size and redd dimensions will be assessed using an underwater video system suspended from a boat. The camera will be lowered to a fixed distance off the bottom and measurements will be made using a calibrated grid attached to the monitor. Monitoring and Evaluation Plan 10

16 The data will be transmitted to the USFWS for HSC development. The HSC for fall-run Chinook salmon, spring-run Chinook salmon, and steelhead will be used in combination with 2-dimensional hydraulic modeling to develop relationships between flow and amounts of spawning and incubation habitat in known spawning areas. Task 1-2. Spawning and Egg/Alevin Distribution Existing information on the timing and distribution of fall-run Chinook salmon, spring-run Chinook salmon, and steelhead spawning and incubation in the lower Yuba River will be reviewed and described. 1 Potential sources of spawning information include: fall-run Chinook salmon spawning escapement surveys (Jones & Stokes ); spring-run Chinook salmon and steelhead redd surveys conducted in 2000 (Jones & Stokes unpublished data); fall-run Chinook salmon, spring-run Chinook salmon, and steelhead redd surveys conducted (U.S. Fish and Wildlife Service unpublished data); spring-run redd surveys conducted in (California Department of Water Resources unpublished data); and steelhead redd surveys conducted as part of this monitoring program (Task 1-1). The results will be summarized as frequency distributions (percent of total redds or spawning adults) by reach and time period (see first table in Figure 2). Annual variation in spawning timing and distribution will be described. In addition to the spatial and temporal distribution of spawning, the duration of the egg incubation and alevin (pre-emergent fry) will be considered in assessing the magnitude of potential redd dewatering impacts. The duration of egg and alevin life stages is important because it determines the fraction of total egg production that has reached the emergent fry stage (and, thus, able to leave the redd) and the remaining fraction that is still present in redds as eggs or alevins (and, thus, vulnerable to dewatering). These fractions will be determined from historical daily water temperatures in specific spawning reaches and time periods, and published relationships between daily water temperatures and emergence times for Chinook salmon and steelhead/rainbow trout (e.g., Beacham and Murray 1990; Crisp 1981, 1988). Each group of eggs (defined as the proportion of eggs deposited in redds in a given reach and time period) will be 1 The characterizations of Chinook salmon as fall-run and spring-run may not be accurate, depending on whether or not these two runs are genetically distinct and can be distinguished on the basis of spawning time. Monitoring and Evaluation Plan 11

17 tracked separately, and the proportion of total egg production remaining in the redds in each successive time period will be determined using the daily water temperatures in that reach and the predicted fry emergence dates. The computational steps are illustrated in the first 3 boxes in Figure 2. Task 1-3. Redd Dewatering Analysis The redd dewatering evaluation will be based on the results of effective habitat analysis, to be conducted by the USFWS as part of their instream flow study. Effective habitat analysis, a modeling option of the Physical Habitat Simulation (PHABSIM) component of the Instream Flow Incremental Methodology (IFIM), provides a means of determining the percentage of usable spawning habitat that remains suitable for survival of eggs and pre-emergent fry after a given flow reduction (Harlow pers. comm.). To evaluate potential redd dewatering impacts, the USFWS proposes to use geographic information systems (GIS) in combination with the habitat output of a 2-dimensional hydraulic model to determine percent changes in effective spawning habitat (measured in terms of weighted usable area) as a function of flow (Harlow pers. comm.). Effective habitat is defined as the percentage of usable spawning habitat meeting specific incubation criteria (minimum depths and velocities) following a flow reduction. In the absence of relationships between survival and hydraulic conditions over redds, it will be assumed that conditions for incubation and emergence will become unsuitable if the tailspill of the redd is exposed or if velocities drop to levels below those selected by adult salmon for spawning. The minimum suitable redd depth for each species and run will be defined as the average difference between the measured redd and tailspill depths. Because it is assumed that female salmon choose redd sites that maximize the survival probability of their offspring, the minimum suitable velocity will be defined as the lowest velocity where redds are found. The results of the effective habitat analysis will be based on 10 study sites selected by the USFWS for modeling the spawning habitat of fall-run Chinook salmon, spring-run Chinook salmon, and steelhead (U.S. Fish and Wildlife Service 2002). These sites were selected because they represent areas of heaviest spawning use. Because the results of effective habitat analysis are based on selected study sites, the results may not be representative of all spawning areas in a given spawning reach. However, it can reasonably be assumed that the channel and hydraulic characteristics of these sites are representative of preferred spawning areas based on the high spawner use of these sites. Jones & Stokes will use the results of the effective habitat analysis in combination with the spawning and egg/alevin distribution data (Task 1-2) to evaluate potential redd dewatering impacts associated with various flow reductions. The percentage of total egg production in each reach at the time of a specific flow reduction will be multiplied by the reduction in effective spawning habitat (expressed as a fraction of the total usable spawning habitat before the flow reduction) to generate an index of potential redd dewatering. The computational steps are illustrated in the last 3 boxes of Figure 2. The index Monitoring and Evaluation Plan 12

18 Spawning Distribution % Total Adults or Redds Reach Oct 1 7 Oct Oct Oct Oct 29 Nov Water Temperature Mean Daily Water Temperature ( C) Reach 1-Oct 2-Oct 3-Oct 4-Oct 5-Oct Relationship between temperature and hatching/emergence times Egg/Alevin Distribution % Total Egg Production in Redds Reach Oct 1 7 Oct Oct Oct Oct 29 Nov Reduction in Effective Spawning Habitat % Reduction in Weighted Usable Area (%WUA) Reach cfs cfs cfs cfs cfs Index of Potential Redd Dewatering % Total Egg Production in Redds x %WUA Reach cfs cfs cfs cfs cfs Figure 2 Steps Used to Compute Redd Dewatering Index for Specific Flow Reductions

19 would be summed over all affected reaches to generate an overall index of potential redd dewatering. The following equation will be used to compute indices of potential redd dewatering for specific flow reductions and times of the year: n RDI = ((WUA ib - WUA ia )/WUA ib ) x E it ) i=1 where: RDI = redd dewatering index. WUA ib = usable spawning habitat in reach i before flow reduction WUA ia = effective spawning habitat in reach i after flow reduction E it = percentage of total egg production in gravel (percent of total) in reach i at time t n = total number of reaches subjected to flow reduction The redd dewatering index is an indicator of the maximum potential impact assuming that all usable spawning habitat is used by adults. The actual impact may vary depending on the actual use of available spawning habitat in any given year (number and distribution of redds). Task 2. Fry Stranding Monitoring and Evaluation Task 2-1. Aerial Photography and Mapping Stereo aerial photographs of the entire lower Yuba River (RM 0 RM 24) were taken in August 2002, February 2003, and May 2003 at the following flows: 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 Monitoring and Evaluation Plan 13

20 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, This orthophotograph will serve as a common photographic base for habitat mapping. The photographs were 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 boundaries (wetted shoreline) 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. Task 2-2. Stranding Area-Flow Relationships The aerial photographs and digital shoreline maps will be examined to determine the type, location, extent, and status (e.g., isolated or not isolated from the main river) of potential fry stranding sites at each of the documented flows. Specific sites will be classified according to the following definitions: Side channel (SC) Secondary channels formed along the lateral margins of bars that are typically separated from the main channel at low flow. Backwater (BW) Relatively large pools formed along the lateral margins of bars by sediment deposition, beaver dams, and other obstructions. Pothole (PH) Small, isolated depressions typically caused by local scouring around obstructions (e.g., woody vegetation) on bar surfaces. Low-gradient bar (LGB) Bars with <5% slopes (to be determined from slope maps generated from the digital terrain model). GIS software will be applied to the digital shoreline maps to measure the water surface area of individual sites at each target flow. Area measurements will be summed according to the following formula: n SA = A i i=1 where: SA = potential stranding area A i = water surface area of site i Monitoring and Evaluation Plan 14

21 n = total number of potential stranding sites The results will be used to develop relationships between flow and the distribution, extent, and status of potential stranding sites. These relationships will be described in tables, graphs, and maps. Task 2-3. Fry Distribution Existing information will be used to describe the timing and distribution of Chinook salmon and steelhead fry rearing in the lower Yuba River. The predicted spatial and temporal distribution of fry emergence will serve as a basis for predicting the initial distribution of fry. The initial distribution of fry is considered a relatively sensitive indicator of the stranding potential in a given reach and time period because of the relatively high susceptibility of this life stage to stranding. Estimates of the spatial and temporal distribution of emergent fry will be derived from the spawning distributions for each species and the predicted proportions of fry emerging from redds during the incubation period (Task 1-2). The range of variability in timing and distribution of fry emergence will also be described based on observed variability in spawning distributions and water temperatures. Additional sources if information will be used to describe the spatial and temporal distribution of fry following emergence. Potential sources include: descriptions of the timing and distribution of Chinook salmon and steelhead spawning (Task 1-2); fish community surveys during (Beak Consultants 1989; Jones & Stokes 1992; Jones & Stokes file memoranda); downstream migrant trapping in (California Department of Fish and Game, Jones & Stokes unpublished data); fish salvage records from the Hallwood-Cordua fish screen during (California Department of Fish and Game unpublished data); juvenile steelhead surveys in (Jones & Stokes, Kozlowski unpublished data); and fish stranding surveys conducted in previous years (Jones & Stokes 1992, 1998, 1999) and as part of the current monitoring and evaluation program (Task 2-4). Because the data from each source are not directly comparable and are influenced by annual variability in fry abundance, the results from each source and year will be reviewed independently and summarized in terms of presence/absence or relative abundance of fry and juveniles (depending on the types and quality of data collected) by reach and time period. The results will then be used to describe the overall longitudinal and seasonal patterns of occurrence and relative abundance of fry in the lower Yuba River. The results will be expressed in terms of presence/absence or percent of total fry population. Reported relationships Monitoring and Evaluation Plan 15

22 between environmental variables (e.g., habitat type) and fry distribution, abundance, and size will also be described. Task 2-4. Fry Stranding Survey Field surveys will be conducted to determine the occurrence (presence or absence) and relative abundance of fry in potential stranding sites before, during, and after scheduled flow reductions. Before a scheduled flow reduction, the stranding area-flow relationships (Task 2-2) will be used to identify specific sites where fry may become stranded. These sites will be the focus of fry stranding surveys. Potential stranding sites will be surveyed to determine the occurrence and extent of fry isolation (associated with the magnitude of the flow reduction) and bar stranding of fry (associated with ramping rate). These surveys will also provide an opportunity to verify the interpretation of aerial photographs, measure site characteristics that influence fish stranding (e.g., water depths), and add to existing information on the spatial and temporal distribution of fry in the lower Yuba River. The primary survey method will be visual observation (wading or snorkeling). Potential stranding areas more than about 1-foot deep will be searched by snorkeling, and areas less than about 1-foot deep will be searched by wading and snorkeling (a face mask will be used to verify species identification). Because of substantial differences in habitat conditions among potential fish stranding sites (e.g., depth, substrate, cover), no single method or combination of methods is likely to provide comparable estimates of fish abundance among sites. Differences in vulnerability of different species and sizes of fish to different capture methods also contribute to this problem. Furthermore, because of the need to survey a number of sites over much of the river s length immediately following a flow change, the use of intensive abundance estimation methods (e.g., removal, mark-recapture) would be impractical. Therefore, the primary objective of this task will be to determine the presence or absence of stranded fry. However, indices of abundance will be computed by dividing the observed number of fish by the surveyed area. These indices will be useful for making general comparisons of fish abundance among reaches and seasons. The occurrence and relative abundance of fry in off-channel habitats will be determined by surveying these sites immediately before and immediately after a scheduled flow reduction. Field crews will consist of two persons experienced in snorkeling and fish identification. One or both persons (depending on site width) will start at the downstream end of each site and work slowly upstream, searching the entire site for fish. In large side channels or backwaters, counts will be made along 3 4 band transects spaced at equal intervals across the width of the site. The width of each transect will depend on visibility, which will be determined by measuring the distance from a person s position to the farthest point at which he or she can clearly distinguish an object similar in shape and size to a small salmon or steelhead (50 millimeters [mm]). The number and size class (<100 mm and >100 mm) of Chinook salmon and steelhead will be recorded on plastic slates. Monitoring and Evaluation Plan 16

23 The occurrence and relative abundance of fry in potential bar stranding areas will be determined by surveying low-gradient bars immediately before and during scheduled ramping events ranging from cfs per hour. Because of the short duration of the ramping period (one to several hours), manpower constraints will limit observations to several sites that can be effectively monitored during the ramping period. To maximize efficiency, these sites will be pre-selected based on their proximity to each other and Englebright Dam, the abundance of fry, and the range of bar slopes present at these sites. Preferred sites will be low-gradient bars with relatively high fry densities and bar slopes ranging from 0 5%. Slope maps generated from the digital terrain model will be used to identify potential monitoring sites. These sites will be limited to the upper portion of the Garcia Gravel Pit reach (above the Highway 20 bridge); ramping rates are likely to be highest in this reach because of the attenuation of flow changes with increasing distance from Englebright Dam. An effort will be made to limit these sites to a 1- to 2-mile segment of river to minimize the travel time between sites during the ramping period. Before a scheduled ramping event, 3 5 monitoring sites will be selected using the criteria above. Because of their relatively large surface area, the selected bars will be surveyed for fry using the same sampling methods described above for large side channels or backwaters. A surveying rod and level will be used to measure the slope of the bars at several locations to determine the range of bar slopes present at each site. For large bar areas that cannot be completely searched, band transects measuring 5 10 feet in width will be established perpendicular to the shoreline (extending from the existing shoreline to the predicted shoreline location after the flow reduction) at three locations representing the range of bar slopes. Two field crews consisting of 2 persons each will be positioned at two of the selected bars at the beginning of the ramping event. As flows recede and the bar is exposed, the crew will search the exposed portion of the transect and record the number, size, and species of stranded fish. Searching will include turning over gravel and cobble to determine the presence of fish below the surface. Following a period of minutes of searching at one site, the crews will travel by boat to the nearest site and begin searching the transects there for another minutes before moving on to another site or back to the original site (depending on the total number of sites). This will continue until the ramping event has ended and all sites have been searched. Physical habitat conditions will be documented at potential stranding areas before, during, and after scheduled flow reductions. Temporary staff gages will be placed in all off-channel and bar stranding sites where stranding is being monitored. Automated water temperature recorders will be installed in the offchannel habitats and the main river adjacent to these sites. Sketches will be drawn and photographs taken to document the dimensions, general habitat features, and degree of isolation of each site. The degree of isolation and ability of fry to return to the main river will be visually assessed based on fish size (i.e., body depth) and the depth, continuity, and direction of flow between each site and the main channel. A survey rod and level will be used to measure the gradient of the channel or bar linking the site with the main channel. A hip chain will be used to measure the length and average width (based on a series of width Monitoring and Evaluation Plan 17