BATTLE CREEK HYDROELECTRIC PROJECT FERC NO LICENSE AMENDMENT APPLICATION APPENDIX 5 OPERATIONS EFFECTS ON ANADROMOUS FISH

Transcription

1 BATTLE CREEK HYDROELECTRIC PROJECT FERC NO LICENSE AMENDMENT APPLICATION APPENDIX 5 OPERATIONS EFFECTS ON ANADROMOUS FISH Operations Effects on Anadromous Fish

2 APPENDIX 5 OPERATIONS EFFECTS ON ANADROMOUS FISH Table of Contents 1 INTRODUCTION... A Hydroelectric Project Description... A Current Project Description... A Proposed Facility Modifications... A Proposed Instream Flow Modifications... A Hydroelectric Project Water Routing... A Current Project... A Phases 1A and 1B... A Phase 2... A Ecological Process Changes... A METHODS... A Water Temperature... A Migration Habitat... A Barriers... A Entrainment in Diversions... A Predation, Pathogens, and Food... A LONG-TERM AND ONGOING EFFECTS... A Key Habitat Quantity Substantial Increase in Spawning and Rearing Habitat Area in Response to Increased Minimum Instream Flow Requirements... A Water Temperature Substantial Increase in Survival during Spawning and Rearing Life Stages in Response to Cooler Water Temperatures... A Migration Habitat... A Substantial Increase in Survival of Adults and Increased Spawning Success in Response to Higher Instream Flows... A Substantial Increase in Survival of Adults and Increased Spawning Success in Response to Removal of Five Dams and Construction of More-Reliable, Effective Fish Ladders... A Potential Increase in Spawning Success and Fry Production in Response to Separation of the Powerhouse Water Discharge from the Natural Stream Channel... A Entrainment Substantial Increase in Survival of Juvenile Steelhead and Chinook Salmon during Downstream Movement and Migration as a Result of Elimination of Some Diversions and Construction of Fish Screens at the Remaining Diversions... A Predation, Pathogens, and Food Reduction of Predation-Related Mortality as a Result of Removing Dams and Improving Fish Ladders... A Substantial Increase in Production of Food for Fish Resulting from Increased Minimum Instream Flows... A FACILITY MONITORING PLAN... A REFERENCES... A PERSONAL COMMUNICATIONS... A5-117 A5-i

3 List of Tables TABLE A5-1. RESTORATION PROJECT COMPONENTS... A5-5 TABLE A5-2. TABLE A5-3. PHASES 1A AND 1B RESTORATION PROJECT MONTHLY MINIMUM INSTREAM FLOW REQUIREMENTS... A5-6 PHASE 2 RESTORATION PROJECT MONTHLY MINIMUM INSTREAM FLOW REQUIREMENTS... A5-7 TABLE A5-4. EFFECTIVE FLOWS AT FISH LADDERS UNDER THE PROPOSED ACTION... A5-30 TABLE A5-5. TABLE A5-6. TABLE A5-7. TABLE A5-8. TABLE A5-9. DISTRIBUTION OF POTENTIAL NATURAL BARRIERS AND DIVERSION DAMS THAT MAY IMPEDE UPSTREAM FISH PASSAGE... A5-31 CALCULATED SPAWNING AREA (ACRES) FOR PEAK MONTHS OF STEELHEAD AND CHINOOK SALMON LIFESTAGE OCCURRENCE FOR MINIMUM FLOW REQUIREMENTS (BASELINE VS. PHASES 1A AND 1B)... A5-35 CALCULATED REARING AREA (ACRES) FOR PEAK MONTHS OF STEELHEAD AND CHINOOK SALMON LIFESTAGE OCCURRENCE FOR MINIMUM FLOW REQUIREMENTS (BASELINE VS. PHASES 1A AND 1B)... A5-37 ESTIMATED SURVIVAL OF CHINOOK SALMON EGGS IN RESPONSE TO WATER TEMPERATURE DURING INCUBATION AT VARIOUS LOCATIONS IN BATTLE CREEK UNDER BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-54 ESTIMATED SURVIVAL OF STEELHEAD EGGS IN RESPONSE TO WATER TEMPERATURE DURING INCUBATION AT VARIOUS LOCATIONS IN BATTLE CREEK UNDER BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-57 TABLE A5-10. ESTIMATED SURVIVAL OF JUVENILE CHINOOK SALMON IN RESPONSE TO WATER TEMPERATURE DURING REARING AT VARIOUS LOCATIONS IN BATTLE CREEK UNDER BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-60 TABLE A5-11. ESTIMATED SURVIVAL OF JUVENILE STEELHEAD IN RESPONSE TO WATER TEMPERATURE DURING REARING AT VARIOUS LOCATIONS IN BATTLE CREEK UNDER THE BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-63 TABLE A5-12. POTENTIAL STEELHEAD AND CHINOOK SALMON PASSAGE OVER NATURAL BARRIERS IN BATTLE CREEK FOR MINIMUM REQUIRED INSTREAM FLOWS 1 UNDER BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-69 TABLE A5-13. EFFECTIVE FLOWS AT FISH LADDERS FOR THE RESTORATION PROJECT... A5-71 A5-ii

4 TABLE A5-14. PRIOR 15 YEARS OF POWERHOUSE OUTAGES ( ) AND APPROXIMATE RESULTING CHANGE IN FLOW IN THE POTENTIALLY AFFECTED BATTLE CREEK PROJECT REACHES BY RESTORATION PROJECT PHASE... A5-76 TABLE A5-15. SUMMARY OF FACILITY AND INSTREAM FLOW MODIFICATIONS FOR BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-108 TABLE A5-16. APPROXIMATE SUMMER STREAM SURFACE AREA (ACRES) BY REACH FOR MINIMUM REQUIRED INSTREAM FLOWS FOR BASELINE CONDITIONS AND THE RESTORATION PROJECT... A5-113 A5-iii

5 LIST OF FIGURES FIGURE A5-1. ESTIMATED AVERAGE JULY WATER TEMPERATURE FOR SELECTED LOCATIONS ON BATTLE CREEK, MINIMUM INSTREAM FLOW REQUIREMENTS UNDER BASELINE CONDITIONS AND FOR THE RESTORATION PROJECT... A5-14 FIGURE A5-2. ESTIMATED AVERAGE MONTHLY WATER TEMPERATURE AT COLEMAN DIVERSION DAM, MINIMUM INSTREAM FLOW REQUIREMENTS UNDER BASELINE CONDITIONS AND FOR THE RESTORATION PROJECT... A5-15 FIGURE A5-3. ESTIMATED AVERAGE MONTHLY WATER TEMPERATURE AT COLEMAN DIVERSION DAM, MINIMUM INSTREAM FLOW REQUIREMENTS UNDER BASELINE CONDITIONS AND FOR THE RESTORATION PROJECT... A5-16 FIGURE A5-4. ESTIMATED AVERAGE MONTHLY WATER TEMPERATURE AT THE MOUTH OF NORTH FORK BATTLE CREEK, MINIMUM INSTREAM FLOW REQUIREMENTS UNDER BASELINE CONDITIONS AND FOR THE RESTORATION PROJECT... A5-17 FIGURE A5-5. ESTIMATED AVERAGE MONTHLY WATER TEMPERATURE ON MAINSTEM BATTLE CREEK, MINIMUM INSTREAM FLOW REQUIREMENTS UNDER BASELINE CONDITIONS AND FOR THE RESTORATION PROJECTKEY HABITAT QUANTITY... A5-18 FIGURE A5-6 RESPONSE OF DEVELOPING WINTER-RUN CHINOOK EMBRYOS TO TEMPERATURE... A5-23 FIGURE A5-7. RESPONSE OF DEVELOPING SPRING-RUN CHINOOK EMBRYOS TO TEMPERATURE... A5-24 FIGURE A5-8. RESPONSE OF OVER-SUMMERING SPRING-RUN CHINOOK SALMON ADULTS TO TEMPERATURE... A5-25 FIGURE A5-9. RESPONSE OF DEVELOPING WINTER-RUN CHINOOK SALMON JUVENILES TO TEMPERATURE... A5-26 FIGURE A5-10. TEMPERATURE TOLERANCE OF CHINOOK SALMON SMOLTS... A5-27 FIGURE A5-11. TEMPERATURE TOLERANCE OF STEELHEAD SMOLTS... A5-28 FIGURE A5-12. STEELHEAD TROUT SPAWNING AND REARING HABITAT ON THE KESWICK REACH OF NORTH FORK BATTLE CREEK... A5-39 FIGURE A5-13. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE NORTH FORK BATTLE CREEK FEEDER REACH OF NORTH FORK BATTLE CREEK... A5-40 FIGURE A5-14. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE EAGLE CANYON REACH OF NORTH FORK BATTLE CREEK... A5-41 A5-iv

6 FIGURE A5-15. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE WILDCAT REACH OF NORTH FORK BATTLE CREEK... A5-42 FIGURE A5-16. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE SOUTH REACH OF SOUTH FORK BATTLE CREEK... A5-43 FIGURE A5-17. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE INSKIP REACH OF SOUTH FORK BATTLE CREEK... A5-44 FIGURE A5-18. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE COLEMAN REACH OF SOUTH FORK BATTLE CREEK... A5-45 FIGURE A5-19. CHINOOK SALMON AND STEELHEAD TROUT SPAWNING AND REARING HABITAT IN THE MAINSTEM REACH OF BATTLE CREEK... A5-46 FIGURE A5-20. WATER TEMPERATURE EFFECTS ON NORTH FORK BATTLE CREEK BELOW EAGLE CANYON DIVERSION DAM... A5-66 FIGURE A5-21. WATER TEMPERATURE EFFECTS ON SOUTH FORK BATTLE CREEK BELOW SOAP CREEK CONFLUENCE... A5-67 A5-v

7 1 INTRODUCTION The foundation for the Battle Creek Salmon and Steelhead Restoration Project (Restoration Project) was set out in 1999 through the signing of a Memorandum of Understanding (MOU) by the U.S. Department of the Interior, Bureau of Reclamation (Reclamation), the U.S. Fish and Wildlife Service (USFWS), the National Oceanic and Atmospheric Administration, National Marine Fisheries Service (NMFS), the California Department of Fish and Game (CDFG), and the Pacific Gas and Electric Company (Licensee). The signatories to the 1999 MOU have jointly proposed to undertake the Restoration Project. The proposed Restoration Project presents an opportunity to reestablish approximately 42 miles of prime salmon and steelhead habitat on Battle Creek, plus an additional 6 miles of habitat on its tributaries. Restoration would be accomplished primarily through the modification of the Battle Creek Hydroelectric Project s (Federal Energy Regulatory Commission [FERC] Project No. 1121) (Hydroelectric Project) facilities and operations, including instream flow releases. The Restoration Project includes modifications to facilities at nine dam sites located on North Fork Battle Creek, South Fork Battle Creek, Baldwin Creek, Lower Ripley Creek and Soap Creek. The MOU signatories have decided to implement these modifications in Phases, each of which has independent ecological and environmental benefits. This license amendment application seeks approval to implement Phase 1A only. An Action Specific Implementation Plan (ASIP) has been prepared for the Restoration Project on behalf of Reclamation, the lead agency overseeing the design and construction of the Restoration A5-1

8 Project, and the FERC, as a cooperating agency responsible for ensuring that the proposed changes and continued operation of the Hydroelectric Project comply with the federal Endangered Species Act (ESA). The ASIP is intended to serve as the biological assessment (BA) for the Restoration Project for both Reclamation and FERC. The ASIP provides the information necessary for NMFS to analyze the potential effects of the Restoration Project on anadromous fish, including the Central Valley spring-run Chinook salmon, Sacramento River winter-run Chinook salmon, Central Valley fall-/late fall run Chinook salmon, and Central Valley steelhead, and designated critical habitat for Central Valley spring-run Chinook salmon and Central Valley steelhead. This appendix describes effects on anadromous fish and their habitat in the North Fork and South Fork Battle Creek that may occur as a result of long-term operations associated with the Hydroelectric Project after completion of Phases 1A, 1B, and 2 of the Restoration Project. The following sections provide a general description of the proposed modifications for each Phase of the Restoration Project, the water routing after implementation of each Phase, the methods used to determine effects of the Restoration Project on anadromous fish and anadromous fish habitat, the measures that would be implemented to minimize and mitigate any adverse effects, the monitoring plan for facilities, and the adaptive management processes that would be implemented to ensure the success of the Restoration Project. Information on species occurrence and status, life histories of special-status anadromous fish, and factors affecting species abundance are presented in Section 4.1, Fish, in Volume I of the final EIS/EIR (Jones & Stokes 2005). Most of the information provided below is also set out in the final EIS/EIR (Jones & A5-2

9 Stokes 2005), the draft ASIP (Jones & Stokes 2004), and the Adaptive Management Plan for the Restoration Project (Terraqua Inc. 2004). 1.1 Hydroelectric Project Description Current Project Description The Hydroelectric Project was initially developed in the early 1900s. The Hydroelectric Project consists of five powerhouses (Volta, Volta 2, South, Inskip, and Coleman), two small upstream storage reservoirs (North Battle Creek and Macumber), three forebays (Grace, Nora, and Coleman), five diversions on North Fork Battle Creek (Keswick, Al Smith, North Battle Creek Feeder, Eagle Canyon, and Wildcat), three diversions on South Fork Battle Creek (South, Inskip, and Coleman), numerous tributary and spring diversions, and a network of some 16 canals, ditches, flumes, tunnels, and pipelines. The Hydroelectric Project was acquired by the Licensee in It was initially licensed by the Federal Power Commission in 1932 and was relicensed by FERC in 1976 for a period of 50 years. The current FERC License sets the minimum instream flow requirements at 5 cubic feet per second (cfs) in South Fork Battle Creek and 3 cfs in North Fork Battle Creek. Several of the tributaries (Soap, Ripley, and Baldwin Creeks) have no minimum instream flow requirements. For a complete description of the Hydroelectric Project, see Exhibit A of this license amendment application Proposed Facility Modifications Phase 1A will begin with the facility modifications on North Fork Battle Creek, Eagle Canyon Canal, and Asbury Dam. For Phase 1A, fish passage improvements on North Fork Battle Creek A5-3

10 will be achieved by installing fish screens and ladders at the North Battle Creek Feeder and Eagle Canyon Diversion Dams; installing the Eagle Canyon Canal pipeline; removing the Wildcat Diversion Dam and appurtenant conveyance systems; and modifying the Asbury Dam. Phase 1B improvements on the lower South Fork Battle Creek include installing a tailrace connector from Inskip Powerhouse to Coleman Canal and a new Inskip Powerhouse bypass. For Phase 2, additional fish passage improvements on the South Fork Battle Creek are proposed by removing the South, Soap Creek Feeder, Lower Ripley Creek Feeder, and Coleman Diversion Dams; installing a fish screen and ladder on the Inskip Diversion Dam; installing a tailrace connector from South Powerhouse to Inskip Canal; and decommissioning the South Canal. Table A5-1 summarizes the individual components of each Phase of the Restoration Project Proposed Instream Flow Modifications Modifications to instream flows are a key component of the Restoration Project. The Battle Creek Working Group (BCWG) Biological Technical Team collaborated on the development of a detailed minimum flow release schedule for each dam. That team included biologists from the fishery agencies and PG&E, and participants from the BCWG. The proposed flow schedule addressed species habitat needs by stream reach and included the flows necessary to address passage and water temperature needs. The minimum instream flows that relate to baseline conditions, Phases 1A and 1B Restoration Project conditions, and Phase 2 Restoration Project conditions, are set forth in Tables A5-2 and A5-3, respectively. A5-4

11 Table A5-1. Restoration Project Components Site Name Component Phases 1A and 1B Phase 2 North Battle Creek Feeder Diversion Dam Eagle Canyon Diversion Dam and Canal Wildcat Diversion Dam, Pipeline, and Canal South Diversion Dam Soap Creek Feeder Diversion Dam Inskip Diversion Dam and South Powerhouse Lower Ripley Creek Feeder Diversion Dam Coleman Diversion Dam and Inskip Powerhouse Asbury Diversion Dam 1 Phase 1B Install fish screen and ladder Set new minimum instream flow for North Battle Creek Feeder reach ranging from 47 to 88 cfs Improve access road Install fish screen and ladder Remove segment of the Eagle Canyon spring collection facility Set new minimum instream flow for Eagle Canyon reach 35 to 46 cfs Improve access trail Replace section of Eagle Canyon Canal with buried pipeline Remove dam, pipeline and canal Improve access roads and trail Construction of Inskip Powerhouse and Coleman Canal connector 1 Replace Inskip Powerhouse bypass 1 Improve access road 1 Install instream flow release monitoring and recording equipment Set minimum instream flow for Baldwin Creek at 5 cfs Modify dam to provide fish barrier Remove dam Remove dam Install fish screen and ladder Construction of South Powerhouse and Inskip Canal connector (tunnel) Set minimum instream flow for Inskip reach ranging from 40 to 86 cfs Remove dam Remove dam A5-5

12 Table A5-2. Phases 1A and 1B Restoration Project Monthly Minimum Instream Flow Requirements Monthly Minimum Flow Release (cfs) Dam JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC North Fork Battle Creek North Battle Creek Feeder Eagle Canyon Wildcat Facility removed; no instream flow requirement South Fork Battle Creek South Inskip Coleman 1 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) 5(30) Ripley Creek Lower Ripley No instream flow requirement Soap Creek Soap No instream flow requirement Baldwin Creek Asbury For Phases 1A and B, the FERC minimum instream flow requirement below Coleman Dam will remain at 5 cfs year-round. The 30 cfs instream flow below Coleman Dam is the result of an Interim Flow Agreement between Reclamation and the Licensee and is not contained in the MOU. After Coleman Dam is removed in Phase 2, there will be no instream flow requirement at that location. A5-6

13 Table A5-3. Phase 2 Restoration Project Monthly Minimum Instream Flow Requirements Monthly Minimum Flow Release (cfs) Dam JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC North Fork Battle Creek North Battle Creek Feeder Eagle Canyon Wildcat Facility removed; no instream flow requirement South Fork Battle Creek South Facility removed; no instream flow requirement Inskip Coleman Facility removed; no instream flow requirement Ripley Creek Lower Ripley Facility removed; no instream flow requirement Soap Creek Soap Facility removed; no instream flow requirement Baldwin Creek Asbury A5-7

14 1.2 Hydroelectric Project Water Routing Current Project The Hydroelectric Project currently diverts water from North Fork and South Fork Battle Creek and several tributaries. Diversions from North Fork Battle Creek are made at North Battle Creek Feeder, Keswick, Al Smith, Eagle Canyon and Wildcat Diversion Dams; diversions from South Fork Battle Creek are made at South, Inskip, and Coleman Diversion Dams. Diversions from South Battle Creek tributaries include Soap Creek Feeder, Upper Ripley Creek Feeder and Lower Ripley Creek Feeder. Diversions from Battle Creek mainstem tributaries include Asbury Diversion Dam. A portion of North Fork water is conveyed from its natural drainage and across a plateau through a series of tunnels, flumes, and open channels to the South Fork. South Fork water is similarly conveyed, although it remains within its natural drainage. Water from the two forks is ultimately collected into penstocks and dropped down to the South, Inskip, and Coleman Powerhouses situated on the north bank of South Fork Battle Creek and mainstem Battle Creek. Occasionally, the powerhouses are shut down because of maintenance or because of lightning strikes, transmission grid disruptions, or other emergencies. When this occurs, the South and Inskip Powerhouse penstock intakes are shut off. In emergency conditions, water in the canals feeding South Powerhouse is discharged via a bypass to South Fork Battle Creek until the diversions into the canals can be shut down. Water in the canals feeding Inskip Powerhouse is diverted via a bypass facility back into South Fork Battle Creek until the diversions into the A5-8

15 canals can be shut down. Water in the canal feeding Coleman Powerhouse also can be discharged into South Fork Battle Creek and mainstem Battle Creek depending on the circumstances and discharge location along the canal. One of the objectives of the Restoration Project is to essentially eliminate the discharge of North Fork Battle Creek water to South Fork Battle Creek above the natural confluence Phases 1A and 1B Water on the North Fork will continue to flow to mainstem Battle Creek and be routed to the South Fork facilities through North Battle Creek Feeder and Eagle Canyon Diversion Dams to the Cross Country Canal and Eagle Canyon Canal, respectively. Wildcat Diversion Dam will be decommissioned. Spring water diversion facilities at Eagle Canyon Diversion Dam will be removed, allowing the spring water to continue to flow into North Fork Battle Creek, eliminating the possibility of diversion of these spring waters into South Fork Battle Creek. South Powerhouse will continue to receive water from Union Canal, a combination of flows from the South and Cross Country Canals and Soap Creek Diversion Dams. After passing through the South Powerhouse, the combined waters will continue to be discharged to South Fork Battle Creek. At this location, water from South Fork Battle Creek can be diverted at the Inskip Diversion Dam to the Inskip Canal and Powerhouse. The Inskip Canal is also fed by the Eagle Canyon Canal and Lower Ripley Creek Diversion Dam. The discharge from Inskip Powerhouse will be passed directly through a newly constructed tailrace connector into Coleman A5-9

16 Canal. Coleman Canal feeds Coleman Powerhouse, situated farther downstream on mainstem Battle Creek. A new Inskip Powerhouse water bypass facility will be constructed (Phase 1B) consisting of three sections: (1) the upland pipeline section beginning at Eagle Canyon Canal; (2) the downslope chute section; and (3) the Coleman Canal connector section. With this bypass system, a shutdown of the Inskip Powerhouse does not affect the continued operation of downstream Coleman Powerhouse and prevents the bypassed water from discharging to South Fork Battle Creek Phase 2 All proposed changes to the facilities located on the North Fork Battle Creek will be completed in Phase 1A. North Fork water will flow to mainstem Battle Creek and be routed to the South Powerhouse through North Battle Creek Feeder and Eagle Canyon Diversion Dams to the Cross Country Canal and Eagle Canyon Canal, respectively. In Phase 2, on South Fork Battle Creek, South Diversion Dam and Canal will be removed, as well as Soap Creek Feeder and Lower Ripley Creek Feeder Diversion Dams. South Powerhouse will continue to receive water from Union and Cross Country Canals. A new tailrace connector will be constructed to pass water from South Powerhouse to the Inskip Canal, eliminating the powerhouse discharge to South Fork Battle Creek. A5-10

17 Water from the South Powerhouse will pass directly to the Inskip Canal, which joins the Eagle Canyon Canal and then feeds the Inskip Powerhouse. South Fork Battle Creek water may also be diverted to Inskip Powerhouse via Inskip Diversion Dam. In Phase 1B the discharge from Inskip Powerhouse will pass directly through the tailrace connector into Coleman Canal. Coleman Canal feeds Coleman Powerhouse. Occasionally, South and Inskip Powerhouses are shut down because of maintenance or because of lightning strikes, transmission grid disruptions, or other emergencies. When this occurs, the associated penstock intake facilities are shut off. In the event the powerhouse and the penstock facilities are shutdown, water in the canals feeding South Powerhouse will be diverted via a bypass facility back into the tailrace connector between South Powerhouse and Inskip Canal. The water in the canals feeding Inskip Powerhouse will be diverted into the newly constructed bypass system (Phase 1B construction). The bypass system will deliver the water to the Coleman Canal and Powerhouse. Water from Coleman Powerhouse is discharged back to mainstem Battle Creek. The bypass systems allow water to continue to be diverted to downstream powerhouses and, together with the tailrace connectors at South and Inskip Powerhouses, essentially eliminate any discharge of North Fork Battle Creek water to South Fork Battle Creek. One exception occurs at an emergency overflow wasteway in the Inskip Canal. It is located in the area between the South Powerhouse tailrace connector tunnel outlet and the diversion from Inskip Diversion Dam. The wasteway consists of a 100-foot-long concrete overflow box and pipe set in the southwestern Inskip Canal embankment and has a capacity of 150 cfs. It is designed to protect Inskip Canal A5-11

18 from an uncontrolled overtopping, which could lead to a canal failure. The Inskip Canal wasteway allows flows that exceed the canal capacity to be spilled from the canal in a controlled manner. Flows may exceed the canal capacity when water is being discharged from the powerhouse and the penstock bypass system and being diverted from South Fork Battle Creek. These circumstances are rare, short in duration, and unintentional. The water discharged from the overflow, a mixture of North and South Fork water, would enter South Fork Battle Creek at this location. 1.3 Ecological Process Changes The goal of the Restoration Project is to restore the ecological processes necessary for the recovery of steelhead and Chinook salmon populations in Battle Creek and to minimize the loss of clean and renewable electricity that may result from modifications to the Hydroelectric Project. The Restoration Project would modify both Hydroelectric Project facilities and operations to provide for water management in Battle Creek consistent with the life cycle needs of anadromous fish. Specifically, the Restoration Project contemplates that the following modifications to the Hydroelectric Project would result in the restoration of ecological processes that support anadromous fish: Adjustments to Hydroelectric Project operations, including allowing cold spring water to reach natural stream channels, reducing the amount of water diverted from streams, and decreasing the rate and manner in which water is withdrawn from the stream and returned to the canals and powerhouses following outages. Modification of facilities, such as fish ladders, fish screens and bypass facilities, diversion dams, and canals and powerhouse discharge facilities to improve passage and stabilize habitat conditions. Changes in the approach used to manage the Hydroelectric Project to better balance hydroelectric energy production with habitat needs, using ecosystem-based management that A5-12

19 protects and enhances fish and wildlife resources and other environmental values using adaptive management, reliable facilities, and water rights transfers, among other strategies. 2 METHODS An evaluation of the environmental consequences of the long-term operations of the Battle Creek Hydroelectric Project on anadromous fish and their habitats under the Restoration Project was conducted based on a review of existing literature, discussions with fish biologists knowledgeable about the project area, and the findings of the BCWG Biological Technical Team (Kier 1999). The long-term effects of the Hydroelectric Project were found to be associated with permanent and ongoing changes in environmental conditions. Monthly models were used to simulate the predicted habitat area and water temperature regime in the project area under the minimum flows that would be in place under the Baseline Conditions and under Restoration Project conditions (Figures A5-1 A5-5). The modeling compared two sets of minimum flow requirements and resultant temperature regimes, as follows: 1. The baseline minimum flow requirements represent the existing FERC license flow requirements and are 3 cfs below the North Fork Battle Creek diversion dams and 5 cfs below the South Fork Battle Creek diversion dams. Cold water from springs is captured by canals and does not enter adjacent stream reaches. 2. The Restoration Project minimum flow requirements, which were established under the 1999 MOU, are substantially higher than the baseline flow requirements. Cold water from springs is allowed to flow into adjacent stream reaches. The flow prescription varies throughout the season by reach depending on the life history requirements of the three species that are the primary focus of restoration activities and may be adjusted pursuant to an Adaptive Management Program described in the Adaptive Management Plan (Appendix 2). A5-13

20 Figure A5-1. Estimated Average July Water Temperature for Selected Locations on Battle Creek, Minimum Instream Flow Requirements under Baseline Conditions and for the Restoration Project A5-14

21 Figure A5-2. Estimated Average Monthly Water Temperature at Coleman Diversion Dam, Minimum Instream Flow Requirements under Baseline Conditions and for the Restoration Project A5-15

22 Figure A5-3. Estimated Average Monthly Water Temperature at Coleman Diversion Dam, Minimum Instream Flow Requirements under Baseline Conditions and for the Restoration Project A5-16

23 Figure A5-4. Estimated Average Monthly Water Temperature at the Mouth of North Fork Battle Creek, Minimum Instream Flow Requirements under Baseline Conditions and for the Restoration Project A5-17

24 Figure A5-5. Estimated Average Monthly Water Temperature on Mainstem Battle Creek, Minimum Instream Flow Requirements under Baseline Conditions and for the Restoration ProjectKey Habitat Quantity A5-18

25 Methods for evaluating key habitat quantity rely on minimum flow requirements for each of the alternatives based on the assumption that the minimum flow at any time can limit the fish population. During the wet season the flow is above minimum values at unpredictable times in unpredictable amounts as influenced by runoff events. Streamflow directly influences the availability and function of important habitat elements, including water velocity, depth, wetted area, and cover. Flow-habitat relationships for Battle Creek are based on the Instream Flow Incremental Methodology (IFIM) and Physical Habitat Simulation (PHABSIM) system (Milhous et al. 1984; Thomas R. Payne and Associates 1998a). Streamflow and release of cold water from springs into adjacent stream reaches also influence the water temperature regime. PHABSIM and the USFWS Instream Flow Temperature Model (SNTEMP) temperature studies were applied to on-site studies on Battle Creek as part of the Upper Sacramento River Fisheries and Riparian Habitat Management Plan process (Upper Sacramento River Fisheries and Riparian Habitat Advisory Council 1989). A comprehensive study that predicted habitat quantity as a function of flow and temperature was conducted under the guidance of a technical committee that included biologists from the fisheries agencies and Licensee (Thomas R. Payne and Associates 1998a). The flow-habitat relationships that were identified by the study were integrated with the temperature model and analyzed by the BCWG Biological Technical Team in a public forum (Kier 1999, Kier 1998). The analysis identified: 1. The priority species and life stages of focus for each reach of Battle Creek based on the usability of the reach determined from the predicted temperature regime and life history functions for five species of anadromous salmonids at a particular time of year; A5-19

26 2. The requisite flows to facilitate each species upstream access over obstacles in the stream channel based on migration timing; 3. The appropriate rates of flow changes to avoid stranding and isolation of juveniles; and 4. The water temperatures influenced both by increased flows and releases of cold spring fed water to adjacent reaches of Battle Creek. The instream flow releases at each of the dam sites developed through this process became the MOU and Restoration Project flows, and the ramping rates used after power system outages are also those identified in the MOU and Restoration Project. In addition, the MOU and Restoration Project also specify a time of year for planned outages that is least likely to cause risks attributable to ramping operations. Spawning and rearing habitat area was calculated for the baseline conditions and Restoration Project minimum flow requirements. 2.1 Water Temperature As water temperature increases toward the extremes of the tolerance range of a fish, biological responses, such as impaired growth and risk of disease and predation, are more likely to occur (Myrick and Cech 2001; Sullivan et al. 2000). Once temperatures exceed the tolerance range for a species at a certain life stage, survival decreases depending on the magnitude and duration of the elevated temperatures. Different life stages and species have different temperature responses, and the tolerance ranges that are identified in available literature are relatively broad (see the discussion under Section 4.1, Fish, in the final EIS/EIR [Jones & Stokes 2005]). Conclusive studies of the thermal requirements completed for Chinook salmon and steelhead in Central A5-20

27 Valley streams are limited (Myrick and Cech 2001), but for the purposes of this assessment of effects, survival estimates focus on the most temperature-sensitive life stages at the times of year when these life stages are both present and vulnerable because of climate conditions. Temperature response survival estimates are based on studies reported in the literature and impact analysis techniques used for the same assemblage of fish in the Sacramento River. The presence and absence of temperature-sensitive life stages are based on results of life history studies in the nearby Sacramento River and results of trapping and survey estimates on Battle Creek that have produced juvenile and adult abundance indices (U.S. Fish and Wildlife Service 2001). Monthly average water temperature was simulated for the months of June through September under the minimum flow requirements in each reach of Battle Creek for each alternative using SNTEMP (Pacific Gas & Electric Company 2001) (for details, see Appendices K and R of the final EIS/EIR [Jones & Stokes 2005]). It should be noted that the daily temperatures will vary throughout the month, causing the actual mortality relationships to vary throughout the month as the fish respond to daily average temperatures; however, the performance of the two alternatives on average over a month was used to provide a suitable comparative analysis. Temperature thresholds for survival and suitability for the different life stages of the priority species for the Restoration Project are presented as follows: Winter-run Chinook salmon embryos in June (Figure A5-6) and spring-run Chinook embryos in September (Figure A5-7) when the most temperature-sensitive pre-eyed life stage is at peak abundance and warm climate conditions occur. With respect to winter-run, mortality in July also will continue to be significant because of effects of elevated temperatures on this life stage; however, the relative differences between the No Action and the preferred alternative in July are considered to be similar to those in June. Temperature-survival relationships indicated on the figures are those developed for the same assemblage of A5-21

28 Chinook salmon in the nearby upper Sacramento River for use in a similar impact analysis for a temperature control project (U.S. Fish and Wildlife Service 1990; U.S. Department of the Interior, Bureau of Reclamation 1991). These temperature-survival relationships were applied to Battle Creek in the Restoration Plan (Kier 1999) and confirmed for winter run in later studies by the USFWS. Spring-run Chinook salmon adults over-summering in August (Figure A5-8) when warm climate conditions occur and the adults are reaching the end of the pre-spawning holding period when energy reserves are low. The temperature response indicated on the figures includes the preferred temperature range (California Department of Water Resources 1988) and a range where the exposure represents stressful conditions. The relationships were presented in the Battle Creek Restoration Plan (Kier 1999). Winter-run Chinook salmon juvenile temperature tolerance in September (Figure A5-9) when this life stage is present and warm climate conditions occur. The temperature response indicated in the figures includes lethality (Brett 1952; Raleigh et al. 1984; Myrick and Cech 2001) and preferred temperature range (Groot and Margolis 1991). Literature covering the response for exposure to temperatures between lethal and preferred shows considerable variation; factors that increase the difficulty of replicating a response include food availability (Bisson and Davis 1976) and acclimation temperature (Brett 1952). Spring-run Chinook salmon and steelhead smolt thermal tolerance in June (Figures A5-10 and A5-11) when the last of these smolt populations are present (U.S. Fish and Wildlife Service 2001; Brown pers. comm.) and warm climate conditions occur. The temperature response indicated in the figures refers to the advanced juvenile life stages of anadromous salmonids when the parr stage transforms to smolt (smoltification) during the spring. Changes in behavior and physiology prepare the smolts for survival in saltwater. Based primarily on controlled experiments, water temperatures high enough to interrupt the smoltification process vary by species (see reviews by Wedemeyer et al. 1980). From literature reviews, Zedonis and Newcomb (1997) identified three categories of thermal tolerance for salmonid smolts for the Trinity River. The three categories optimal, marginal, and unsuitable were defined by the relative likelihood that smolts would revert to parr or lose their ability to osmoregulate in seawater. Studies examining relationships between water temperature and smoltification for steelhead have observed a reduction in migratory tendencies in response to elevated temperatures (greater than 55.4ºF) (Zaugg 1981) and reduced physiological changes at higher temperatures (59ºF) that were inferred to be associated with a sharp decline in the number of outmigrating wild steelhead smolts captured in traps (Kerstetter and Keeler 1976). A5-22

29 Figure A5-6 Response of Developing Winter-run Chinook Embryos to Temperature A5-23

30 Figure A5-7. Response of Developing Spring-run Chinook Embryos to Temperature A5-24

31 Figure A5-8. Response of Over-Summering Spring-Run Chinook Salmon Adults to Temperature A5-25

32 Figure A5-9. Response of Developing Winter-Run Chinook Salmon Juveniles to Temperature A5-26

33 Figure A5-10. Temperature Tolerance of Chinook Salmon Smolts A5-27

34 Figure A5-11. Temperature Tolerance of Steelhead Smolts A5-28

35 It will not be possible to develop reliable production estimates for the target species until additional detailed temperature data are developed that provide daily average temperature over the year for the Battle Creek watershed. In the meantime, critical factor analysis for temperature response examines the most temperature-sensitive life stages at the most vulnerable period of the year to compare alternatives. In addition, the analysis indicates the reaches of streams at various times of the year that the various life stages may be obligated to use in order to survive at reasonable levels in response to temperature. 2.2 Migration Habitat Barriers Migration habitat includes the specific conditions that support migration of individuals to spawning and rearing habitat, in particular the upstream migration of adult Chinook salmon and steelhead. Delay and multiple attempts at passing the dams or natural barriers may reduce the survival of adults because of injury and exhaustion. After failed attempts at passing a dam, adults may spawn downstream of the dams or natural barriers, where survival of eggs may be reduced by warmer water temperature. Methods for evaluation of migration habitat are qualitative. Minimum required flows under each alternative are used to assess the potential for impedance of migration. The effective flow range for fish ladders is used to determine the potential for passage impedance at all dams (Table A5-4). For natural barriers (Table A5-5), Thomas R. Payne and A5-29

36 Associates (1998b) determined flows that would allow fish passage at all low-flow barriers. Flows less than the minimum passage flow are assumed to impede upstream migration. Table A5-4. Effective Flows at Fish Ladders under the Proposed Action Name of Diversion Dam Effective Flow Range (cfs) North Battle Creek Feeder Diversion Dam 4 4 to Eagle Canyon Diversion Dam 4 20 to 71 1 Wildcat Diversion Dam 4 South Diversion Dam Dam removed Dam removed Inskip Diversion Dam to 170 Coleman Diversion Dam Lower Ripley Creek Feeder Diversion Dam Soap Creek Feeder Diversion Dam Dam removed Dam removed Dam removed Kennedy, DWR (2001). Gravel may accumulate in the entrance pool to the fish ladder at Inskip Diversion Dam under the proposed design, leading to an ongoing operations impact between the dam and the ladder. The fish ladder at Inskip Diversion Dam could function at (as yet unspecified) lower flows if the orifices were blocked (Kennedy, DWR 2001). Phase 1A Although the minimum passage flows are based on field observation of potential barriers (Thomas R. Payne and Associates 1998b), the actual impedance of migration is uncertain, and adult steelhead and Chinook salmon undoubtedly would pass many of the barriers at lower flows or take advantage of peaks in runoff. A5-30

37 Table A5-5. Distribution of Potential Natural Barriers and Diversion Dams That May Impede Upstream Fish Passage Location (River Mile) North Battle Creek Type of Barrier/Name of Dam Absolute Barrier Falls/Cascade Falls Falls/Cascade Cascade/Chute Falls Falls/Cascade Falls/Cascade Falls/Cascade Rock Creek 9.92 Falls North Battle Creek Feeder Diversion Dam Falls Falls Falls/Cascade Eagle Canyon Diversion Dam Falls Wildcat Diversion Dam Falls Subsurface Flow South Battle Creek Absolute Barrier South Diversion Dam Cascade Inskip Diversion Dam Falls/Cascade/Chute Falls/Cascade Falls/Cascade/Chute Falls Coleman Diversion Dam Distance to Next Downstream Barrier (miles) A5-31

38 False Attraction In addition to flow barriers, mixing of North Fork Battle Creek flow with South Fork Battle Creek flow potentially results in false attraction of adult Chinook salmon and steelhead from their natal reaches in North Fork Battle Creek. Water temperature in North Fork Battle Creek is cooler than in South Fork Battle Creek. Water temperatures required for spawning and rearing of steelhead and Chinook salmon are more likely to be adverse in South Fork Battle Creek, especially from April through October. Reproductive failure of adults that stray to South Fork Battle Creek may reduce the overall year class production for Battle Creek as a whole, depending on the level of habitat saturation in North Fork Battle Creek. The mechanisms that allow salmonids to home properly generally stem from their ability to recognize the olfactory characteristics of their home stream (Hasler and Scholz 1983). Juvenile salmonids remember, or imprint on, the smell of organic compounds that are uniquely characteristic of a given stream or stream reach. When returning to fresh water to spawn, adult salmonids use these odors to locate and return to the stream reach where they were hatched and reared. Homing may be influenced by such factors as flow, water temperature, presence of other salmon, and habitat quality (Pascual and Quinn 1994; Quinn 1984, 1997). For instance, the homing precision of salmon increases with the relative magnitude of streamflow present in the home stream (Hindar 1992). Evaluation of the potential for false attraction is qualitative. The proportion of the flow in South Fork Battle Creek that comprises flow discharged from North Fork Battle Creek is assumed to A5-32

39 indicate the potential for false attraction (that is, false attraction is assumed to increase when there are higher proportions of North Fork Battle Creek flow in South Fork Battle Creek). 2.3 Entrainment in Diversions Diversions entrain fish encountering the intake. Fish diverted into the hydropower canals are assumed to suffer total mortality and not contribute to annual production for the species populations in the stream. For reaches upstream of a diversion point, the proportion of production entrained is assumed equal to the proportion of streamflow diverted. Simulated flows and diversions under each alternative are used to assess the potential entrainment (for details, see Section 4.3, Hydrology, in the final EIS/EIR [Jones & Stokes 2005]). Fish screens that function at design and performance criteria are expected to avoid most losses of juvenile Chinook salmon and steelhead attributable to entrainment and impingement. 2.4 Predation, Pathogens, and Food Analysis of potential effects on predation and pathogens is qualitative. Dams and the associated fish ladders and other facilities are assumed to increase predation above natural levels, potentially increasing the abundance of predators and disorienting prey. Increased abundance of Chinook salmon and steelhead is assumed to increase the occurrence of salmonid pathogens in Battle Creek. Analysis of food effects is similarly qualitative. Prey abundance affects growth rate and the survival of individual fish. Prey abundance may increase with increased stream surface area. The minimum required flows under each alternative are used to estimate stream surface area and A5-33

40 assess relative differences in prey-species production (for details, see Section 4.3, Hydrology, in the final EIS/EIR [Jones & Stokes 2005]). 3 LONG-TERM AND ONGOING EFFECTS Long-term and ongoing effects fall into five categories: key habitat quantity; water temperature; migration habitat; entrainment in diversions; and predation, pathogens, and food. Long-term and ongoing effects associated with implementing the Hydroelectric Project as modified by the Restoration Project are described below. 3.1 Key Habitat Quantity Substantial Increase in Spawning and Rearing Habitat Area in Response to Increased Minimum Instream Flow Requirements The Restoration Project will increase the minimum instream flow requirements in multiple reaches of Battle Creek throughout Phases 1and 2 of the Restoration Project, which is expected to have a substantial beneficial effect on steelhead and Chinook salmon and on essential fish habitat (EFH) for Chinook salmon. The increased flow will increase spawning and rearing habitat area for steelhead, spring-run Chinook salmon, winter-run Chinook salmon, and fall-/late fall run Chinook salmon (Tables A5-6 and A5-7, Figures A5-12 through A5-19). As shown in Tables A5-6 and A5-7, the total spawning and rearing habitat areas will be several times greater than the current area after implementation of each phase of the Restoration Project. A5-34

41 Table A5-6. Calculated Spawning Area (Acres) for Peak Months of Steelhead and Chinook Salmon Lifestage Occurrence for Minimum Flow Requirements (Baseline vs. Phases 1A and 1B) Reach of Battle Creek Baseline Steelhead Spawning Area a Spring-Run Chinook Spawning Area b Winter-Run Chinook Spawning Area c Keswick 0.06 North Battle Creek Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Restoration Project Phases 1A and 1B Keswick 0.06 NBC Feeder Eagle Canyon Wildcat South Inskip Coleman e Main e Total Late Fall-Run Chinook Spawning Area d Note: If the removal of a dam under an alternative precludes the need for a minimum flow requirement, the minimum flow requirement for the adjacent upstream or downstream dam is applied. a Values are for the month of February. b Values are for the month of September. c Values are for the month of June. d Values are for the month of March. e Values are from Appendix H (Tables H1 and H6) of final EIS/EIR. A5-35

42 Table A5-6. Continued Reach of Battle Creek Baseline Steelhead Spawning Area a Spring-Run Chinook Spawning Area b Winter-Run Chinook Spawning Area c Keswick 0.06 North Battle Creek Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Restoration Project Phase 2 Keswick 0.06 NBC Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Late Fall-Run Chinook Spawning Area d Note: If the removal of a dam under an alternative precludes the need for a minimum flow requirement, the minimum flow requirement for the adjacent upstream or downstream dam is applied. a Values are for the month of February. b Values are for the month of September. c Values are for the month of June. d Values are for the month of March. A5-36

43 Table A5-7. Calculated Rearing Area (Acres) for Peak Months of Steelhead and Chinook Salmon Lifestage Occurrence for Minimum Flow Requirements (Baseline vs. Phases 1A and 1B) Reach of Battle Creek Baseline Steelhead Rearing Area a Spring-Run Chinook Rearing Area b Winter-Run Chinook Rearing Area c Keswick 1.92 North Battle Creek Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Restoration Project Phases 1A and 1B Keswick 1.92 NBC Feeder Eagle Canyon Wildcat South Inskip Coleman e Main e Total Late Fall-Run Chinook Rearing Area d Note: If the removal of a dam under an alternative precludes the need for a minimum flow requirement, the minimum flow requirement for the adjacent upstream or downstream dam is applied. a Values are for the month of July. b Values are for the month of February. c Values are for the month of October. d Values are for the month of July. e Values are from Appendix H (Tables H1 and H6) of final EIS/EIR. A5-37

44 Table A5-7. Continued Reach of Battle Creek Baseline Steelhead Rearing Area a Spring-Run Chinook Rearing Area b Winter-Run Chinook Rearing Area c Keswick 1.92 North Battle Creek Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Restoration Project Phase 2 Keswick 1.92 NBC Feeder Eagle Canyon Wildcat South Inskip Coleman Main Total Late Fall-Run Chinook Rearing Area d Note: If the removal of a dam under an alternative precludes the need for a minimum flow requirement, the minimum flow requirement for the adjacent upstream or downstream dam is applied. a Values are for the month of July. b Values are for the month of February. c Values are for the month of October. d Values are for the month of July. A5-38

45 Figure A5-12. Steelhead Trout Spawning and Rearing Habitat on the Keswick Reach of North Fork Battle Creek A5-39

46 Figure A5-13. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the North Fork Battle Creek Feeder Reach of North Fork Battle Creek A5-40

47 Figure A5-14. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the Eagle Canyon Reach of North Fork Battle Creek A5-41

48 Figure A5-15. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the Wildcat Reach of North Fork Battle Creek A5-42

49 Figure A5-16. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the South Reach of South Fork Battle Creek A5-43

50 Figure A5-17. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the Inskip Reach of South Fork Battle Creek A5-44

51 Figure A5-18. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the Coleman Reach of South Fork Battle Creek A5-45

52 Figure A5-19. Chinook Salmon and Steelhead Trout Spawning and Rearing Habitat in the Mainstem Reach of Battle Creek A5-46