NOAA National Marine Fisheries Service’s (NMFS)

NOAA National Marine Fisheries Service’s (NMFS)
Biological and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project National Research Council Committee on Sustainable Water and Environmental Management in the California Bay-Delta January 25, 2010

Status of Species ESU Status
Sacramento River winter-run Chinook salmon Endangered (Jan 1994) Central Valley spring-run Chinook salmon Threatened (Sep 1999) Central Valley fall-run Chinook salmon Candidate (Sep 1999) Central Valley steelhead Threatened (Mar 1998) Southern DPS green sturgeon Threatened (Apr 2006) Southern Resident killer whale Endangered (Nov 2005) We are also consulting on endangered Southern Resident Killer Whales There were listed as endangered in 2005 85 whales were counted in 2008, in three pods These whales travel up and down the coast and prefer to eat Chinook salmon. NMFS analyzed project effects on all Central Valley Chinook salmon stocks, as they affect the food base for SRKW.

Central Valley Salmon Population Over Time

Salmon Population Viability
ABUNDANCE POP GROWTH RATE DIVERSITY SPATIAL STRUCTURE HABITAT CAPACITY AND DIVERSITY Freshwater Estuarine Marine

Central Valley Spring Chinook ESU Structure

Central Valley Steelhead ESU Structure
Suisun Bay Tribs identified in the figure (in pink) belong in the Central California Coast steelhead DPS.

Viability Criteria for Populations

Viability Criteria for ESUs
At least two viable populations per diversity group If possible, the populations should not have highly correlated risks of catastrophic disturbance

Current Status of CV Spring- Run Chinook salmon

Climate Change

Effects of Water Projects on Salmon

Effect of Habitat Modification
s

Institutional Challenges

Summary Central Valley Salmonid ESUs are threatened with extinction
Water project facilities and operations have negative effects on fish habitat, with cascading effects on spatial structure, diversity, productivity, and abundance of populations Improving in-stream flows and curtailing exports is necessary to conserve salmon, but will not be sufficient for recovery An ecosystem perspective is needed to understand how human activities impact salmon Adaptive management is needed to reduce risks

Scope of today’s presentation
Brief highlights of Opinion – not all topics presented due to time constraints Opinion itself is a summary document of over four years of analytic work between 5 agencies Biological assessment, NMFS technical memos, peer review reports are important 700+ scientific citations Administrative record is 150,000 pages - - documents full decision-making process Now our presentation will turn to the Biological Opinion. I’d like to start by making a few brief comments about what we are presenting to you today in this powerpoint, versus what is in the Opinion Our goal, given the time constraints, is to provide you with a very brief overview of the Opinion. We’ll just be scratching the surface. Also, we know that the presentation is uneven; by that I mean it does not summarize all portions of the Opinion in equal detail. In preparing for today, we found that summarizing four years of work between five agencies in two hours is very challenging. We are concerned you will have many more questions than answers at the end of today, not to mention at the end of tomorrow, but we are gong to do our best to give you the highlights. We are happy to point towards documents to provide more information on specific topics, and follow up with you to answer questions if there is an opportunity to do so. The Opinion is over 1,000 pages and is itself a summary document. The analysis and conclusions in the Opinion rely on the larger administrative record. This record includes the Biological Assessment, prepared by the Bureau of Reclamation, which is 1200 pages w/o appendices (approx 1300 additional pages for appendices), and contains many of the modeling results that we relied on. Also of importance, are technical memos that support development of specific RPA actions. The Opinion contains over 700 scientific citations, and the administrative record, which has been submitted to the court, and is the basis for legal review of the opinion, is over 150,000 pages.

Approach to Biological Opinion: Challenges
Complexity - geographic scope Multi-species State and federal project – combined operations Number of dams and diversions Economic importance of project Urban water supply, agricultural water supply, commercial salmon fishery Long-term proposed operations (21 years) Litigation history Current events (recession, drought, fishery closure) This is one of the most complex Section 7 consultations NMFS has ever conducted. And we faced several important challenges in completing the consultation. First, the geographic scope is immense. Most Section 7 consultations analyze the effects of one project, like a new bridge or diversion. This consultation, in contrast, is on the continued combined operations of the state and federal SWP/CVP. It Includes analyzing the combined effects of operations on (XX number ) of major facilities up and down the Central Valley, including Shasta reservoir operations on the North, to Folsom and Nimbus operations on the American River, Delta facilities and New Melones operations on the Stanislaus river. (((covering more than xxxxx square miles of ))). Also aging infrastructure, and the need for technological changes. Also, this was a Multispecies consultation including – 5 species under NMFS jurisdiction and Delta smelt under FWS jurisdiction. Multi-jurisdictional because not just USBR, but also DWR – operating under a coordinated operating agreement The project has a very high level of economic importance, given water supply and effects on Fall run Chinook, the major stock of the commercial Pacific salmon industry. We were attuned to those economic forces throughout the course of the consultation. Also, the Bureau of Reclamation asked us to consult on continued long-term operations: the project agencies decided to remove some of previous environmental protections from the project description, and include full build out for contracted supplies, even if that water hadn’t routinely been delivered. Again, I want to make it very clear that no forward-looking conservation measures were included in the project description – those discussions were and are on-going through Bay-Delta Conservation program, but they were not ripe for inclusion in this consultation. This is a very litigious area. The previous 2004 opinion was invalidated by the federal court. All the agencies had a strong desire to develop a legally sustainable opinion. Therefore, we were very careful about our legal side-boards on our analysis and our administrative record. Finally, current events: -- The ongoing drought in California—3 dry to critically dry years -- The recent severe crash in Central Valley fall-run Chinook salmon stocks, and the resultant second consecutive year of total closure of the commercial and recreational salmon harvests.

Approach to Biological Opinion: Constraints
Our task – Limited to analyzing the Federal action, as proposed Uncertainty in science; risk is balanced in favor of the species Reasonable and Prudent Alternative (RPA) – Limited to actions within authority and discretion of USBR and DWR Minimum to avoid jeopardy; NOT a recovery plan Must avoid jeopardy in short-term and long-term Not necessary to prove quantitatively This slide highlights some of the constraints to the analysis. You’ll hear more about each of these as we get into the details. First, our task was to analyze continued project operations on listed species. Consistent with the legal framework of Section 7, other stressors, such as water quality, and nonnative predation are included in the baseline. These stressors ARE important for these species. But they are not the subject of this consultation. Second, despite the wealth of publications on the Delta, this is a highly variable system, where the uncertainty in science is inevitable and accepted part of the analysis. The section 7 process does not require NEW science to be developed. Rather, it requires us to analyze existing data, and where there is uncertainty, use our best professional judgment and balance the risk in favor of the species. Third – As discussed in the earlier presentation on the section 7 consultation process, we were constrained in several important ways in developing the Reasonable and Prudent Alternative. Actions have to be within the authority and discretion of USBR and DWR. Also, the actions are the minimum to avoid jeopardy – that is an appreciable reduction in the likelihood of survival and recovery. They are NOT recovery actions. NMFS has published a draft recovery plan with actions that go far beyond the RPA in scope and anticipated benefits to the species. The actions must demonstrate that jeopardy is avoided in the short-term and the long-term – this is really key: we cannot wait until a new technology is developed and proven to work, if another alternative is available in the short-term. Also, NMFS is frequently in the position where people want to know quantitatively exactly how effective the RPA will be in offsetting effects. We are rarely able to provide that answer. Rather the RPA is designed to minimize the most significant adverse effects.

Consultation Process Used a team of experienced federal biologists and hydrologists. Adhered closely to legal requirements, agency guidelines, and used the best available scientific and commercial information Maintained close and meaningful collaboration with the U.S. Bureau of Reclamation, CA Department of Water Resources, U.S. Fish and Wildlife Service, and CA Department of Fish and Game Draft opinion peer reviewed by CALFED Independent Science Panel and Center for Independent Experts (CIE) Again, this was a four year long process. We used a team of Federal biologists and hydrologists many of whom have a great deal of experience in California’s Central Valley. We supplemented this team with over 30 additional NMFS experts working part time involved in discrete tasks in the consultation. NMFS SWR closely followed all legal requirements and agency guidelines as well as SWR regional guidelines for conducting formal consultation to insure that the final opinion is thoroughly reviewed and that the best available scientific and commercial information was used in analyzing the effects of the action on listed species We started with a Biological assessment given to us by US Bureau of Reclamation – the vast majority of information we used in our analysis was provided to us by Reclamation. NMFS has maintained close collaboration with the Bureau of Reclamation and DWR as well as the U.S. Fish and Wildlife Service and the California Department of Fish and Game throughout the consultation process in developing this biological opinion We are relied on top scientists outside of NMFS to critique our draft Opinion to ensure it is solidly grounded in the best available science. A draft of the opinion was peer reviewed by the CalFed Independent Science Board and the Center for Independent Experts prior to completion of the final opinion. NMFS made significant changes to the Opinion in response to the peer review reports, and we have a technical memo that summarizes those changes if you are interested.

Scientific Evidence Used best scientific and commercial information
Literature review citations Information from previous listing decisions, critical habitat rules, etc. USBR’s Biological Assessment, including model outputs Draft recovery plan Monitoring reports A section 7 consultation is not an endeavor that involves conducting original research. Rather, it relies primarily on the action agency’s biological assessment and summarizes existing information. We reviewed existing literature, and previous compilations including (BiOp starting on page 62): -- NMFS documents, like final rules for listing, critical habitat, previous Opinions, fall-run collapse, ocean productivity, declarations, climate change -- OCAP BA, and the references within it -- References from the various reviews and peer review reports -- data: California Data Exchange Center (CDEC) data, Corps data, CDFG’s Grand Tab database -- Modeling: OCAP BA, requests to Reclamation, “in house” with Derek Hilts -- Literature: electronic literature searches using several electronic databases available through NMFS’ Northwest Fisheries Science Center (NWFSC) and U.C. Davis. Reports developed by the Science center, Calfed Science Program and the Interagency Ecological Program, as well as data bases of DFG, and DWR. Anything about Information Quality Act? Again – mentioned peer review to make sure we got it right,.

Consultation Background
NMFS OCAP biological opinions: Feb. 14, 1992, limited to winter-run Chinook salmon , interim opinions issued due to changes in operations and new species listed October 22, 2004: In 2008, Federal court invalidated that Opinion, and ordered that NMFS prepare a new Opinion. June 4, 2009: Six complaints filed to date. Close coordination with the USFWS throughout the OCAP consultation process My presentation will provide a brief overview of the OCAP consultation, including the background, analytical approach, environmental baseline, major effects, and the reasonable and prudent alternative (RPA). My presentation will be followed by more detailed descriptions of our effects analysis from other presenters. Background and consultation history (NMFS Opinion page 30) 1A Analyzed project impacts only on winter-run Chinook salmon (only listed fish at that time). It was a jeopardy opinion that initiated temperature control requirements in the Sacramento River and extended gates-out periods at Red Bluff Diversion Dam to improve fish passage and survival past this facility. 1B ; several amendments; 2000; 2001; ; 2004 Supplemental 1C. October 22, Analyzed impacts on winter-run, spring-run, and CV steelhead, and did not find jeopardy for any of these species. A lawsuit was filed by a coalition of environmental groups challenging the 2004 opinion, and in April of 2008 federal Judge Wanger ruled that portions of the opinion were “arbitrary and capricious.” Reinitiation of formal consultation was already underway (requested on April 26, 2006) at the time of Judge Wanger’s ruling as a result of changes in the proposed action. Also new species listed and new critical habitat designated. 1D. In December of 2008, NMFS provided the Bureau of Reclamation with a draft OCAP Opinion, finding jeopardy for a number of ESA-listed species. The final Opinion was due on March 2, 2009, but the court granted a 90-day extension, then a 2-day extension until June 4, 2009, to complete the Opinion. 2. As you will hear in a later presentation, NMFS and the FWS coordinated closely throughout the consultation process.

Peer Reviews of the Draft Biological Opinion
CALFED Science Panel: James J. Anderson, University of Washington & Columbia Basin Research Mike Deas, Watercourse Engineering, Inc. Philip B. Duffy, Climate Central, Inc.; University of California, Merced Daniel L. Erickson, Consultant Reg Reisenbichler, Retired--U.S. Geological Survey (USGS) Kenneth A. Rose, Louisiana State University Peter E. Smith, Retired--USGS CIE reviewers: Richard A. Marston Ian A. Fleming E. Eric Knudsen CIE—Center for Independent Experts Key quote from CALFED review: “In general, we found the assumptions to be clearly stated and reasonable, and the information and data used in analyses to be current. The convincing accumulation of individual effects at the life stage level related to project operations, the poor general state of the populations, and the requirement to resolve doubt in the favor of the species, led the panel to conclude that NMFS’ conclusions were robust.” CALFED & CIE reviews supported NMFS overall conclusions

Peer Reviews of the Draft Biological Opinion (cont’d)
Significant changes made in response to peer review recommendations: Editing for clarity and consistency between division analyses Estimate ranges of loss from compilation of existing studies, even when we did not have complete data sets Assessed risk based on weighting and key lines of evidence Plan for drought sequence – not a single dry year 2. Some of the changes NMFS made between the December 11, 2008, draft and June 4, 2009, final: 2.A. Considerable editing for clarity and consistency between division analyses 2.B. Estimate ranges of loss from compilation of existing studies, even when we did not have complete data sets 2.C. Assessed risk based on weighting and key lines of evidence: Weighted evidence by certainty and magnitude: Considered weight of evidence (high, medium, low), magnitude of effect (high, medium, low), and probable fitness reduction. For all stressors that ranked “high, high” – carried forward into the main lines of evidence leading to jeopardy and adverse mod and at least one action in the RPA list of actions that effectively minimizes this adverse effect. 2.D. Plan for drought sequence of multiple dry or critically dry years – not a single dry year Biggest gap – need to work with our Science Center to develop a quantitative life cycle model that will specifically meet our needs.

Analytical Overview Evaluated each stressor by species, life stage, and location Risk and uncertainty incorporated throughout Weighted evidence by certainty and magnitude of effect Stated assumptions, reviewed model constraints and applicability, used ranges Identified all direct and indirect effects Considered variability in the Bay-Delta ecosystem Summed for individual, population, diversity group and species levels. 1. Evaluation: 1.A. Risk and uncertainty—benefit of the doubt to the species Discussed in previous slide 1.B. 1.C. Identified all potential effects, but focused on high magnitude effects with high weight of evidence Considered variability—no silver bullet Summed effects on individuals, individual effects on the populations, then diversity group, and finally, at the species levels to determine whether the proposed action is likely to jeopardize the listed species or result in the destruction or adverse modification of critical habitats.

HABITAT CAPACITY AND DIVERSITY
Analytical Approach Viable Salmonid Populations ABUNDANCE POP GROWTH RATE DIVERSITY SPATIAL STRUCTURE HABITAT CAPACITY AND DIVERSITY Freshwater Estuarine Marine Analytical approach--NMFS Opinion page 51. As discussed in Steve’s earlier presentation on the VSP concept… One of the key aspect of our analytical approach, shown in this graphic, is the viable salmonid populations concept, based on best available science and confirmed by scientific peer reviews Note that abundance is an indicator and a reflection of population growth rate, diversity, and spatial structure.

Analytical Approach (cont’d)
Central Valley Technical Recovery Team products: Historical population structure Assessing viability of Central Valley salmon and steelhead populations Life cycle approach 1. We also used the technical recovery team products of 1.A. Historical population structure and 1.B. Assessing viability of Central Valley salmon and steelhead populations, to inform our analysis. These reinforced the VSP framework and highlight the importance of securing all extant populations in the Central Valley, because there are so many “missing” populations, or populations that have been extirpated. 2. Consistent with the section 7 process, we used a life cycle approach--Analyzed the effects of the action in a stepwise order: 2.A. reviewed the status of the species, 2.B. defined the baseline, 2.C. analyzed project-related effects, including individual project related stressors (for example, temperature, reverse flows) on each life stage, for each species, in each division, as broken out in OCAP BA. Went through a process where we explicitly accounted for risk and uncertainty, by assessing ranges, and quality of information (as described earlier), 2.D. summed these effects to the risk to the population, 2.E. summed population effects/risks to determine risk to the ESU – is there an appreciable reduction in survival or recovery? Or adverse modification of critical habitat?

Stressors on Listed Species
Loss of habitat and degraded water quality due to: Non-Federal dams and diversions Land use activities Invasive species Hatcheries Harvest activities Environmental variations Ocean conditions Climate change In general, factors responsible for the current status of the species—NMFS Opinion page 134. Project operations are not the only impact on listed fish. Listed fish also impacted by --non-federal dams and diversions, --lack of rearing habitat caused by levees, Invasive species Hatchery effects—hatchery operations can result in dilution of genetic integrity of listed stocks, reduce the fitness of listed stocks and result in increased competition between hatchery and listed stocks Ocean and in-river commercial and recreational fisheries. Ocean conditions and climate change Analysis is based on division, as provided in the OCAP BA

Environmental Baseline
Environmental baseline--NMFS Opinion page 171. Ongoing action—Looked at aggregate of effects, not incremental changes from current operations. Graphical representation of baseline stressors on Chinook salmon [excluding OCAP effects (general baseline stress regime)] that result in mortality, reduced growth, and reduced reproductive success -- freshwater: life history stages affected include adult immigration and holding, spawning, egg incubation, alevin, fry, and fingerling life stages -- Bay/Delta: mainly smolts -- Ocean: sub-adults and adults Climate change: not depicted in the figure, but a baseline stressor expected to exacerbate many of the stressors on anadromous salmonids throughout their life cycle, particularly with respect to water temperature in all environments, inland hydrology, and ocean productivity (e.g., upwelling)

Effects Overview Shasta Reservoir: Future operations, including climate change: 5 to 65% mortality of winter-run Chinook salmon eggs and fry Red Bluff Diversion Dam (RBDD): Delays adult passage of up to 15% of the winter-run and up to 70% of the spring-run that spawn above the RBDD Blocks up to 35% of green sturgeon from its only known spawning ground American River: Mean water temperatures > 65°F, results in increased incidence of disease in juvenile steelhead ~75% of time in June, 100% in July and August, >95% in September Now to jump to a very brief overview of some of the main effects of the action: Shasta Reservoir (NMFS Opinion page 249): future operations is the 2030 scenario of full build out -- climate change scenario is the warmer, more dry scenario RBDD (NMFS Opinion page 242) is an upstream and downstream migration barrier American River (NMFS Opinion page 277): Based on the 82-year record… Modeled mean water temperatures greater than 65ºF for the majority of the time from June through September

Effects Overview (cont’d)
Juvenile survival at export facilities: About 1 in 3 survive through the Federal facilities About 1 in 6 survive through the State facilities Overall mortality in the interior Delta: 35-90% of those that enter interior Delta 5-20% of each winter-run Chinook salmon population Juvenile San Joaquin River steelhead: 90-99% mortality from project and non-project stressors Reduction in approximately 13-15% fall- and late fall-run Chinook salmon, which is killer whale prey; effects from hatchery management. Moving to the Delta (NMFS Opinion page 313)… Overall mortality in the interior Delta includes project (e.g., reverse flows) and non-project (water quality, unscreened diversions, leveed channels, non-native species) stressors Juvenile San Joaquin River steelhead: Project stressors include exports (reverse flows and entrainment) and low flows from Stanislaus River due to New Melones Dam operations Non-project stressors include low flows in Tuolumne, and Merced (FERC licensed projects currently in review), Stockton WWTP, and Port of Stockton related stressors; also leveed channels and lack of riverine habitat. Killer whale prey (NMFS Opinion page 438)—In addition to the effects of the action on the winter- and spring-runs, the action is likely to reduce fall- and late fall-run abundance by 13-15%. Chinook salmon, including all races, from the Central Valley, serve as potential killer whale prey -- Hatchery management for fall-run Chinook salmon

Findings of the Biological Opinion
OCAP would likely jeopardize: Sacramento winter-run Chinook salmon Central Valley spring-run Chinook salmon Central Valley steelhead Southern DPS of North American green sturgeon Southern Resident killer whales Destruction or adverse modification of designated and proposed critical habitat Central California Coast steelhead – not likely to adversely affect this species or its critical habitat Critical habitat: -- Does not include critical habitat for Southern Resident killer whales, which is in the Puget Sound area -- Critical habitat was proposed for Southern DPS of green sturgeon at the time of the consultation

Reasonable and Prudent Alternative (RPA) Overview
Identified actions to alleviate major stressors for each species and summed these for short-term and long-term Included appropriate flexibilities in RPA where possible Monitoring, reporting, research, adaptive management RPA (NMFS Opinion page 575) Earlier, I discussed the risk and uncertainty that we considered, and only those stressors withy high magnitude of effect and high weight of evidence were carried forward in our integration and synthesis of effects, and ultimately, our conclusions. Our RPA was limited to actions that alleviate those major stressors, both in the short and long terms. We’ve also included flexibilities in the rPA, which I will discuss later. Most monitoring and reporting are already in place. Helps with real-time operational decisions, and quantifying the amount of incidental take. The RPA includes a research and adaptive management component, which includes an annual review of the prior water year’s operations and to determine whether any measures prescribed in the RPA should be altered in light of information learned from the prior year’s operations or research, provided that any changes do not limit the effectiveness of the RPA in avoiding jeopardy or adverse modification.

RPA Overview (cont’d) Scope – minimum to avoid jeopardy Themes:
Over 50 individual actions grouped by division, plus a fish passage program Themes: Water quantity and quality gravel augmentation improve passage decrease entrainment engineered solutions 1. Scope: RPA actions were minimum to get the species out of jeopardy and the critical habitat out of adverse modification. Did evaluate feasibility of the RPA through modeling. 1.A. Over 50 actions organized by the 4 divisions and grouped into 5 suites, 1 being for the fish passage program 2. Common themes in the RPA are actions to: Water quantity and quality--decrease water temperatures and provide minimum flow schedules to support the freshwater life stages of the listed species Augment spawning gravel Improve or restore fish passage Decrease entrainment at the Federal and State fish facilities, and Provide engineered solutions [e.g., new pumping plant and fish screen at Red Bluff, new temperature infrastructure at Folsom and Whiskeytown dams, retrofits to existing pumps/salvage facilities, and non-physical barrier (AKA bubble curtain)].

Key Elements of the RPA Clear Creek below Whiskeytown Dam - increased flows and reduced temperatures Shasta Reservoir and the Upper Sacramento River - new temperature management program Shasta Dam - long-term passage prescriptions to allow re-introduction of listed salmon Red Bluff Diversion Dam - interim gate operations until 2012, then gates up all year. Lower Sacramento River basin and Delta - improved juvenile rearing habitat Key elements of the RPA include: 1. Establishing and maintaining essential flows and temperatures in Clear Creek below Whiskeytown Dam 2. A new year-round storage and temperature management program for Shasta Reservoir and the Upper Sacramento River 3. A long-term passage prescriptions at Shasta Dam to allow re-introduction of listed salmon into their native habitat in the Upper Sacramento River watershed 4. At Red Bluff Diversion Dam, interim gate operations of gates down no more than 2 months each year in the short term while an alternative pumping plant is built, and by 2012, gates up all year. 5. To minimize the effects of project and non-project related reductions in the quantity and quality of juvenile rearing habitat in the Sacramento River Basin and Delta, the RPA contains both short-term and long-term actions for improving juvenile rearing habitat in the Lower Sacramento River and northern Delta.

Key Elements of the RPA (cont’d)
American River - New flow and temperature plan; fish passage at Folsom Dam Hatchery Genetics Management Plan for Nimbus Hatchery for steelhead and fall-run Chinook salmon. Stanislaus River – new flow schedule, temperature criteria, and habitat improvements Delta Cross Channel Gates - Additional gate closures during key times when listed fish are likely to be migrating through the area 1. On the American River, the RPA prescribes a flow management standard, a temperature management plan, additional technological fixes to temperature control structures, and in the long-term, fish passage above Folsom dam to restore steelhead to native habitat. 1.A. Development of a Hatchery Genetics Management Plan for Nimbus Hatchery on the American River to improve genetic diversity of both steelhead and fall-run Chinook salmon. 2. On the Stanislaus River, the RPA prescribes a year-round minimum flow regime necessary to minimize project effects to each life-stage of steelhead, including new spring time flows that will support rearing habitat formation and inundation, and create pulses that queue out-migration. The RPA also calls for Reclamation to develop information needed in order to evaluate options for achieving fish passage on the Stanislaus River above Goodwin, Tulloch, and New Melones Dams. 3. Moving down to the Delta, the RPA provides additional gate closures to minimize the diversion of out-migrating juveniles from the north Delta tributaries into the interior Delta through the open Delta Cross Channel gates.

Key Elements of the RPA (cont’d)
Old and Middle Rivers - Flows will be modified to reduce the number of juveniles exposed to the Delta pumps, and fish salvage improvements to reduce mortality San Joaquin Basin - Increased flows and pumping curtailments. Studies – 6 year study of acoustic tagged fish in the San Joaquin Basin to evaluate the effectiveness of the RPA and refine it over the life-time of the project. 1. Within the central Delta, Old and Middle River (entrances to the central Delta) flows will be modified to reduce the number of juveniles exposed to the export facilities, and additional measures will be implemented at the fish facilities themselves to increase survival of fish. 2. Additional measures to improve survival of San Joaquin steelhead smolts include both increased San Joaquin River flows and export curtailments. 3. …and finally, a significant new study of acoustically-tagged fish in the San Joaquin Basin will evaluate the relationship between flow and exports, the effectiveness of the San Joaquin River inflow-to-export ratio action, and to be able to refine it over the life-time of the project.

RPA Flexibilities Real-time operations Phased-in implementation
Performance-based approaches Take limits based on annual juvenile production estimates Actions tiered to water year type/drought exception Research and adaptive management HERE’S AN OPPORTUNITY FOR NMFS TO GET THE MESSAGE OUT THAT THERE ARE many FLEXIBILIITIES BUILT INTO THE RPA. 1. Real-time operations include: -- Monitoring and reporting -- Technical teams (existing and new) that gather and analyze information, and make recommendations, regarding adjustments to water operations within the range of flexibility provided in the RPA actions. For example: ---- Changing the RBDD gate heights for green sturgeon ---- Exact timing of Stanislaus River spring pulse flows – allows them to coincide with flood releases where possible 2. Some examples of phased-in implementation include: -- Interim operations at RBDD of gates in 2 months out of the year before gates out year round in 2012 -- Pilot fish passage program to assess feasibility -- Interim San Joaquin River Inflow to Export ratios, to allow time for the water board and FERC processes to augment flows on non-Federal tributaries 3. Performance-based approaches, like: -- Achieving a range of acreage of rearing habitat without specifying the exact location -- 75% salvage efficiency at the Federal and State fish facilities -- Reducing pre-screen loss at Clifton Court Forebay to no more than 40% 4. Incidental take limit of winter-run based on the predicted size of the population, which allows the project more take if the population improves Water year type/drought exceptions. Examples: -- Shasta actions based on carryover storage levels -- San Joaquin inflow-to-export ratio -- both of the above provide drought exception procedures to protect health and safety 6. Research and adaptive management—I mentioned this earlier. The Opinion allows for adaption with range of prescribed measures, including requiring an annual review with a report of recommended changes from the technical teams. NMFS has recommended using the Calfed Science Program as a partner in conducting this review.

Other Alternative RPA Actions
Evaluated during consultation and rejected (ineffective, critical habitat concerns, smelt concerns, predation issues, etc): Trap and haul of San Joaquin steelhead New screens at the existing pumps New screens in the Delta (e.g., Georgiana Slough) Permanent operable barriers at Head of Old River Non-physical barrier alone at the Head of Old River (without increased flows and export curtailments) As part of the NAS panel’s charge, these are some alternatives to the RPA actions that do not show up in our Opinion, but were analyzed and are part of our administrative record. 1. Trap and haul. Issues include (1) only a few fish in the San Joaquin River, challenge to trap them, and (2) issue with reducing homing instinct, or conversely, straying 2. New screens, rather than retrofitting the existing louvers, at the existing pumps. Issue: Likely cost prohibitive. 3. New screens in the Delta—“no” to Georgiana Slough, but embedded in an engineering solutions action NMFS RPA page 640). Issue: Delta smelt critical habitat Permanent operable barriers as part of the South Delta Improvement project. Issue: Our species critical habitat Non-physical barrier along. Issue: can keep fish in the mainstem San Joaquin River, but still need flows to move the fish out.

Alternatives (continued)
Alternatives to water supply evaluated and included in RPA: Gravel augmentation Rearing habitat restoration Engineered solutions, including: New fish screen at Red Bluff New temperature infrastructure at Whiskeytown and Folsom Dams Retrofits to existing salvage facilities Non-physical barrier (bubble curtain) Where we could, we did provide actions that did not impact water supply. Here are some good examples of that.

Sacramento River Division
I will quickly go over some of the most significant effects in the upstream areas and then the actions used to address them. Bruce Oppenheim

Shasta Dam and Reservoir
Starting with Shasta Storage on page 249 of the NMFS biological opinion (also technical memo). Keswick Dam located 301 miles upstream from delta re-regulates releases from Shasta and Trinity Dams. Trinity River diversions flow thru Whiskeytown Reservoir into Keswick, via the Spring Creek Tunnel, and make up on average 17% of the releases to the Sacramento River.

Carry over Storage in Shasta
Long-term Average Annual and End of September Storage Differences for Shasta Storage, Spring Creek Tunnel Flow, and Keswick Release Difference in Thousands of Acre-feet [TAF] Study Study 6.0 Study Study 7.0 Study Study 7.0 Study Study 7.1 Shasta End-of-September Storage 26 -121 Annual Keswick Release 1 8 6 -2 Annual Spring Creek Powerplant Flows 3 -1 In its simplest terms: End of September storage sets up temperature control for the following summer --Study 6.0: OCAP BA assumptions within the new CalSim-II model framework --Study 7.0: Existing conditions today, at 2005 level of development. --Study 7.1: Existing conditions with near-term future facilities (Inter-tie, Freeport), represents water project demand and operational policy --Study 8.0: Future condition in year 2030 with assumed water demands and policy. --Study 9 suite: Future with climate change and sea level rise. Study 9.0 is the same as Study 8.0 (6 different scenarios). Note that highlighted in red is the long-term average projected reduction in end-of-September storage, both in the near-term and future full build-out scenarios. These are conservative estimates, and could be considerably higher with consideration of climate change. (up to 3x higher) Loss/reduction equates to ~3% of Shasta Reservoir capacity Study 6.0 = 2004 operations Study 7.1 = near future operations Study 7.0 =current operations Study 8.0 = future operations

Calsim and Sacramento River Water Quality Modeling results for temperature exceedances at Balls Ferry under future conditions Study 8.0 76 74 Avg 72 Max 5% 70 10% 68 25% 66 50% 64 75% 90% 62 95% 60 Min Mean Daily Temperature (F) 58 56 54 52 Temperature modeling results based on Calsim II storage estimates Shows Chinook salmon spawning criterion (i.e., 56 degrees) is exceeded in all future years: Likely exceeded 30% of years in August 55% of years in September This has the greatest impact to spring-run Chinook spawning in the mainstem in September, but also winter-run fry that are just emerging from the gravel 50 48 46 44 42 40 38 1/1 1/22 2/12 3/5 3/26 4/16 5/7 5/28 6/18 7/9 7/30 8/20 9/10 10/1 10/22 11/12 12/3 12/24 Date (month/day)

Egg and Fry Mortality by Water Year Type at Balls Ferry
Study 6.0 (2004) Study 7.0 (current) Study 7.1 (near future) Study 8.0 (future) Water Year Type Percent Mortality This shows egg and pre-emergent fry mortality, without climate change in the baseline, based on the temperature modeling Balls Ferry is the compliance location used most often based on Shasta storage in the last 10 years On average mortality is 2-3% However, in critical water years, winter-run mortality doubles from ~ 7% (today) to 15% (near-term future)

Temperature effects with Climate Change
Shows egg & fry mortality when the effects of climate change are INCLUDED in the environmental baseline: 1) Base case scenario here is equal to the future conditions (Study 8 in Calsim) 2) on average, winter-run mortality increase from 2% up to 10% for the drier more warming scenario, and ranges from % in critically dry years. 3) Back to back critical years are expected to be more common under future operations (due to less water available from the Trinity R and higher level of development)

Percent Mortality Water Year Type
Study 6.0 (2004) Study 7.0 (current) Study 7.1 (near future) Study 8.0 (future) Shows spring-run Chinook egg and fry mortality for the mainstem Sacramento River only, without climate change effects in the baseline… Mortality averages 20% in under future operations, and increases to a range of approximately 50 to 65% during the critical years

Percent Mortality Water Year Type
When the effects of climate change are INCLUDED in the environmental baseline… the effects of the future full build out scenario (Study 8.0) increase mortality on average from 20% to 55% (drier more warming scenario) During critical years, mortality increases from 65% in the base case, to 95% under the drier more warming scenario (assumed worse case) Water Year Type

Summary of Significant Effects on the Mainstem Sacramento River
Long-term average loss of 121 TAF September carry-over storage (including effects of climate change) will: Eliminate spring-run spawning in the mainstem Reduce winter-run spawning habitat in the mainstem Increase egg mortality substantially in consideration of climate change [i.e., Critical years increases to 5 to 65% for winter-run, 40 to 95% for spring-run (Sac. R mainstem only), and 4% for steelhead (based on late fall-run Chinook salmon as a surrogate)]. Result in shorter emigration period and lower survival for juvenile salmonids Climate change scenarios assume the worse case Steelhead have significantly lower mortality because they spawn during the winter when there are less temperature impacts on eggs

Red Bluff Diversion Dam (RBDD) Gates in Open Position Looking Upstream
NMFS Opinion analysis starts on page 242 Red Bluff Diversion Dam located 60 miles downstream of Keswick Dam (all winter-run spawn above this point). Gates close from the top down leaving a small gap (less than 18” underneath). This gap has been shown to impinge post-spawn adult green sturgeon that are migrating downstream. In 2007, 11 adults were observed directly killed from gate operations.

4 months closed 2 months closed Shows the timing of runs past RBDD by month. The green box (4 months closed) is the proposed current operation through year 2019. The 2 months closed operation = proposed future operation from The runs most impacted are winter-run, spring-run, and green sturgeon Salmon: due to inadequate fish ladders adult spawners are delayed an average of 21 days this leads to reduced egg viability, and inability to access suitable spawning habitat in tributaries (due to low flows) Green Sturgeon: can’t use fish ladders blockage of up to 35% of the green sturgeon population separates population into 2 artificial groups one above and one below dam during peak of spawning reduced genetic diversity, females separated from males largest, most fecund females are killed trying to pass under gates, reducing number of repeat spawners

Juveniles experience higher predation rates as they pass downstream under the gates
Disoriented Confused by high velocities Can’t avoid predators Past studies have shown juvenile salmon predation is 45-50% during May Also predation in Lake Red Bluff above the diversion gates. Adverse modification of 6 miles of critical habitat from inundation behind RBDD (prime riffle areas for food production flooded).

Effect of Operations on Winter-Run Chinook Salmon
RBDD effects: Gates closed on May 15, precluding passage of up to 15% of the adults Loss of some late season adults reduces egg and juvenile production from the latter part of the run, which reduces overall production Limits juvenile production during the latter part of the spawning season increases juvenile predation of beginning part of outmigration Constriction of the adult run shortens the juvenile outmigration period (limits life history diversity) RBDD effect on adults: Consistent with the paper, “What caused the Sacramento River fall Chinook stock collapse?” (Lindley et al. 2009).

Summary of the Main Effects from Operating RBDD
Adult upstream migration: Delays passage of up to 15% of the winter-run and up to 70% of the spring-run Blocks up to 35% of green sturgeon from its main spawning ground. Juvenile downstream migration: Higher predation rates on juvenile winter-run, steelhead, and green sturgeon as they pass through Lake Red Bluff and the diversion gates (i.e., 45% to 50% during May). Critical habitat: Adverse modification of 6 stream miles from inundation behind RBDD. Green sturgeon adults separated by RBDD, decreases genetic diversity (ability of adults to pair up)

RPA Actions to Address Key Sacramento River Division Effects
Clear Creek: New temperature curtain in Whiskeytown Reduce temperatures in October Shasta Reservoir: Higher Shasta storage required in Sept. & April Shasta Dam: New temperature management program Upper Sacramento River: Long-term passage prescriptions at Shasta Dam to allow re-introduction of listed salmon RBDD gates up, year round by 2012 Lower Sacramento River and Delta: Restore juvenile rearing habitat To minimize the effects of project and non-project related reductions in the quantity and quality of juvenile rearing habitat in the Sacramento River Basin and Delta, the RPA contains both short-term and long-term actions for improving juvenile rearing habitat in the Lower Sacramento River and northern Delta. Decision criteria for temperature management found in Appendix 2-A RBDD conservation measures are in Appendix 2-B Lower Sacramento River restoration in Appendix 2-C

American River Division

Lower American River (LAR)
American River (NMFS Opinion page 277): over 125 miles of riverine habitat was accessible to anadromous fish, now confined to lower 23 miles below Nimbus Dam (85% reduction in habitat) Historically American River supported spring-run Chinook salmon, fall-run Chinook salmon and summer-, fall-, and winter-run steelhead; Now just winter steelhead and fall-run Chinook both of which are dominated by hatchery production (430,000 steelhead smolts is the annual production goal) Consulting on naturally produced steelhead…the hatchery-produced fish are not included in the DPS, but hatchery effects were considered in the opinion. Hatchery steelhead from the American River impact other CV rivers through straying.

Exposure to daily mean water temps
Exposure to daily mean water temps. above 65°F are associated with anal vent inflammation in juvenile steelhead in the LAR June Explain exceedance plots, based on 82-year CalSim record Red line represents 65F, where based on DFG studies steelhead smolts begin to show signs of disease due to temperature Due to increased level of development, demands are projected to increase from 297 TAF in 2005 to 800 TAF by 2030. In 75% of Junes water temperatures would be greater than 65 F In July > 65 F all the time July

August In August > 65 F all the time and approach lethal limits (75 F) about 1-3% of years 50% probability that 70 F would be exceeded under future conditions In September > 65 F 95% of time September

“VSP” = Viable Salmonid Population
Folsom and Nimbus Dams Entrainment Loss of natural river function Flow fluctuations Predation Redd scour Low flows Nimbus hatchery Warm water temps On the American River we don’t have quantitative estimates of mortality like on the Sacramento River, but we know there are multiple important stressors affecting the population. Project stressors impact all VSP components. Point out Nimbus Hatchery is operated to provide a recreational in river fishery, and not to conserve or recover the natural population. Broodstock originated from out of basin, Eel River and several other places. INCREASED WATER DEMANDS: From 2000 through 2006, annual water deliveries from the American River Diversion ranged from 196 TAF in 2000 to 297 TAF in In the OCAP BA, present level water demands for the American River Division were modeled at 325 TAF per year and the 2030 water demands are modeled at nearly 800 TAF per year, an Angling impacts Project Stressors Baseline Stressors

Summary of Main Effects on the Lower American River
Mean water temperatures above 65°F ~75% in June, 100% in July and August, >95% in September, resulting in increased incidence of disease in juvenile steelhead. Reduced genetic diversity from hatchery management program. Little difference between current and future model runs

RPA Actions to Address Key American River Division Effects
New flow and temperature plan; fish passage at Folsom Dam Structural modifications for Improved water temperature control device at Folsom Dam Temperature control curtains at Lake Natoma Temperature control at El Dorado Irrigation District Diversion Hatchery Genetics Management Plan for Nimbus Hatchery for steelhead and Fall-run Chinook salmon. In the short-term the RPA prescribes a flow management standard, a temperature management plan, additional technological fixes to temperature control structures, aimed at improving the coldwater pool behind Folsom Dam. (FMS can be found in Appendix 2-D) The long-term action is to assess fish passage to suitable cold water habitat above the dam. Also, develop a Hatchery Genetics Management Plan for Nimbus Hatchery to improve genetic diversity of both steelhead, and Fall-run Chinook salmon.

New Melones and Stanislaus River operations Rhonda Reed
Eastside Division New Melones and Stanislaus River operations Rhonda Reed

The Eastside Division affects the operations of New Melones Dam on the Stanislaus River, which is one of 3 major tributaries to the San Joaquin River. New Melones Dam is operated in concert with two downstream dams: Tulloch and Goodwin. Goodwin Dam is located at River Mile 59 and is the lowest complete barrier to fish passage. This Division has no TCDs and no hatchery. New Melones has a variety of operational requirements including water deliveries, Delta water quality, as well as fishery needs. This talk only presents the effects of these operations on life history stages of listed Anadromous fish when they occur in the Stanislaus River. Because of time constraints I can’t go into our analysis of the species effects relating to the other tributaries in the basin and how our analysis and RPA actions integrate with Delta actions.

Stanislaus River – New Melones Dam
Listed Species: Central Valley steelhead Southern Sierra Nevada diversity group Current population numbers very low for all 4 populations Stanislaus Tuolumne Merced The anadromous fish species that use the Stanislaus River are CV Steelhead, which is listed under the ESA, and the non-listed CV Fall-run Chinook salmon. Steelhead populations in San Joaquin Basin compose the Southern Sierra Nevada diversity group. Lindley et al 2006 identified 4 historic independent populations in the SJ tribs: Merced, Tuolumne, Stanislaus rivers which are direct SJR tributaries, and the Calaveras river, which enters the estuary on the east side of the Delta. All of these populations are low in numbers. This publication identifies that all of these populations should be conserved to recover the species. Specific to the Stanislaus River, Current steelhead population numbers are very low; and as Dr lindley indicated, the Data are sketchy. Steelhead information is largely collected incidental to sampling directed at fall-run Chinook monitoring, although some direct studies have been done. There is a counting weir for adult migrants which has tended to capture adult Steelhead Juvenile RST (Rotary Screw Trap) trapping for Fall run Chinook typically picks up 6 to 30 outmigrating yearlings each winter/spring Further down in the SJR system at Mossdale, trawl sampling for young salmonids typically captures less than 20 smolts per year, with a unique catch of 40 in 2007. Where direct information for steelhead was not available, fall-run information may have been considered as a surrogate if appropriate. This recognizes key differences in life history, such as both fish will enter the river in the fall, but steelhead spawn later, have different optimal flow/habitat relationships and their juveniles over-summer in the river, whereas fall-run juveniles typically leave the system in spring as young of the year.

Summary of the Main Effects on the Stanislaus River
Temperature Water temperatures too warm for CV steelhead, 3-20% of time , especially May-Sept. The New Melones operational criteria were not well defined in the Project description, so we took the BA modeling results at face value for operational conditions. Our analysis was also informed by the 28 years of New Melones operational data, recognizing that the proposed operations are somewhat different. Key effects on CV steelhead focus on Temperature, Flow and Habitat conditions. With respect to Temperature Monthly Exceedance plots from the BA modeling predict Water temperatures too warm for CV steelhead juvenile rearing 3-20% of the time, especially in May through Sept, and more so in critically dry years.

Temperature Flow Instream flow requirements for CV steelhead not addressed With Respect to Flow Minimum Instream flow requirements for CV steelhead were not addressed in proposed operations. Typical operations drop the flows to sub optimal levels when Stanislaus flows are not needed to meet Delta Water Quality Standards. This typically occurs in January, during spawning, and in September, affecting Juvenile survival; These effects are more pronounced in drier years, but this graphic shows that the summertime drop still occurs in a wet year pattern from The dotted black line represents flows below Goodwin Dam, and the other lines are daily temperature maxima and minima at Orange Blossom Bridge. IFIM – Instream Flow Incremental Methodology (Aceituno 1993)

Impaired Flow Pattern Affects Habitat
Unimpaired Additionally, the impaired flow patterns, depicted in brown, dampen the natural variability of an unimpaired hydrograph. This eliminates migrational cues and also eliminates the fluvial geomorphic processes that maintain steelhead habitat for spawning and rearing. I would like to note that the increased flows that occur in spring and in fall on the impaired hydrograph are salmonid related releases that occurred because of the VAMP agreement in spring and CVPIA b(2) negotiations for the fall attraction flow which are currently negotiated on an annual basis. While the proposed project indicated that these could still be done, there is do definition of how and with what certainty these flows would occur. Impaired

Temperature Flow Ongoing critical habitat degradation Channel incision cuts off rearing habitat Spawning gravel washed out Channel encroachment. The third key effect of NM Ops is ongoing degradation of critical habitat. In 1999, Dr Matthias Kondolf, of UC Berkeley, and his students conducted a reconnaissance level geomorphic assessment of habitat conditions as affected by New Melones operations. This assessment documents channel incision that cuts off rearing habitat, a reduction in spawning habitat, and channel encroachment by riparian vegetation as a result of limiting the frequency and magnitude of geomorphic flows under the post- new Melones operational regime. Ongoing operations will continue this degradation of critical habitat for spawning and rearing; freshwater migration corridors. IFIM – Instream Flow Incremental Methodology (Aceituno 1993)

Modeled Monthly Temperature Exceedance Probability:
July- Orange Blossom Bridge Daily Temperature Variability In formulating the RPA, we looked at defining clearer operational criteria to assure that minimum conditions for steelhead are met in the context of the varied New Melones obligations. For example, with respect to temperature, the BA included modeled monthly temperature exceedance plots as a result of the proposed operations, as shown in the upper figure. Looking at actual data in the lower graph, the temperature tends to vary on a daily basis and the exceedances areas most used by juvenile steelhead, shown by the green to blue plotted lines, generally appear to be not sustained. The effects of sustained high temperatures are more adverse than short-duration high temperatures. This suggests that operations can be adapted to avoid sustained adverse temperature conditions, so the RPA action to address this stressor calls for meeting temperature criteria based on specific life history requirements as New Melones Operations are underway.

Stanislaus River Minimum Steelhead Flows
The RPA actions also prescribe a minimum flow schedule that incorporates seasonal life history needs and is modified depending on the water year type, so that less water is called for in Drier years. Key life history considerations include a pulse flow in the fall to attract adults into the river, winter and spring pulse flows to cue migration and provide access to floodplain habitat, and minimum base flows during spawning and juvenile rearing periods.

Above Normal Releases vs Minimum Flow Schedule
I would just emphasize that these are minimum flows to provide suitable habitat quality. In reality we expect that operational flows will be higher at many times of the year owing to meeting other operational requirements, and some of those flows will serve dual purposes for both another operational need as well as maintaining steelhead. The black line on this graphic is an overlay of the actual operations in an above normal water year, 1999, showing that normal operational releases are generally much higher than the minimum RPA flows. And we also intend that these flow patterns can be adapted to real time conditions, to address temperature needs, flow and habitat conditions, including scheduling geomorphic flows in wet years. Spring pattern can be reshaped for floodplain inundation or, in wet years for geomorphic flows

Channel Demobilization
These flows, coupled with habitat restoration, will reconnect important floodplain habitats and allow geomorphic processes to counter the demobilizing effect of typical operational flows. These photos are from the Kondolf report showing the fossilization of gravel bars and spawning material resulting from the lack of channel maintaining flows. Kondolf, et al. 2001

RPA Actions to Address Key East Side Division Effects
Establish Stanislaus Operations Group Set operational temperature criteria Set minimum flows for steelhead survival Channel maintaining flows in wet years Habitat improvements for spawning and rearing habitat, building on Central Valley Project Improvement Act authorities Assess fish passage past New Melones Dam In Summary the RPA suite of Actions for the Eastside division include actions to more clearly specify operational conditions to reduce adverse effects to steelhead and their habitat. This suite includes: -Establish Stanislaus Operations Group to coordinate implementation of actions and to monitor real time operations to meet temperature criteria and minimum flow patterns for steelhead survival. This includes planning for channel maintaining flows in wet years -The RPA calls for habitat improvements for spawning and rearing habitat, building on Central Valley Project Improvement Act authorities. In the past most of these actions on the Stanislaus River have emphasized fall-run Chinook needs, rather than steelhead. The RPA also calls for Reclamation to develop information needed in order to evaluate options for achieving fish passage on the Stanislaus River above Goodwin, Tulloch, and New Melones Dams. This is prudent given the life-span of the proposed action and the potential for future climate conditions to be warmer and drier. -Assess fish passage past New Melones Dam On the Stanislaus River, the RPA prescribes a year-round minimum flow regime necessary to minimize project effects to each life-stage of steelhead, including new spring time flows that will support rearing habitat formation and inundation and create pulses that queue out-migration.

Delta Division Jeff Stuart

Key Elements in Delta Division
Climate Change DCC Gates Proposed Export Changes Direct Entrainment at Project Facilities Indirect Mortality within Delta San Joaquin River Inflow to Delta Delta (NMFS Opinion page 313): It should be noted that climate change is not part of the proposed project, and will occur in the future regardless of the project’s implementation There were more than a dozen elements in the Delta Division that were described in the proposed project. This presentation will focus on the six elements that are displayed on the screen. I will briefly describe the effects of the elements on the Delta and then explain the RPA actions that address these elements. This presentation is not intended to be an exhaustive review of the Delta Division analysis and RPA actions associated with the opinion.

Temporal Occurrence of Species in Delta
This table illustrates the usage of the Delta by listed fish species and their life history stages. In order to assess the impacts of the proposed project, the spatial and temporal occurrence of the listed fish in relation to the project actions must be identified. Listed fish can be found moving through the Delta in almost any month of the year but typically have peak periods of use, as indicated by the darker cells. For listed salmonids, the greatest use of the Delta typically occurs between December and June, while green sturgeon are present year round. 75

Climate Change Impacts to Delta:
Fall and winter seasons have greatest sensitivity to climate change according to OCAP modeling. Drier climates: In wet years: > risk of pumping entrainment in winter compared to current climate. In dry years: minimal change in OMR flows during winter and spring. Wetter climates: In wet years: < pumping entrainment risk in winter, more positive OMR flows In dry years: > risks in the winter , slightly more negative OMR flows 1) Climate changes are projected to have impacts on the Project’s effects in the Delta region. 2) Most changes are predicted to occur during the fall and winter according to the CALSIM Modeling. 3) In the drier climate scenarios, more pumping occurs in wetter years when water is available than in drier years when water quality issues take precedence. 4) Wetter climates are better. There is more positive OMR flows in AN and Wet Water year types, but the dry cycles have increased pumping effects in winter thus a more negative OMR. 5) Although there are no specific RPA actions for climate change, since it is not an element of the project, actions to reduce entrainment, prevent movement of fish into the delta interior, and enhance migratory flows will aid listed salmonids in the future conditions. 76

DCC Gate Operations S E W DCC Gates N Sacramento River
The DCC gates are located on the Sacramento River near the town of Walnut Grove. The two radial gates are located on the outside bend of the Sacramento River, with a short channel leading up to them. Sweeping velocities are greater on the outside bend of the river compared to the inner bend, and fish densities are biased towards the outside bend of the river. This spatial distribution of the emigrating salmon in the river channel makes them vulnerable to diversion into the DCC channel when the gates are open and water is moving through the gate structures. River flow is also tidally influenced and flows can reverse in this segment of the river, changing the hydrodynamics around the gate inlet.

DCC Gates Manmade channel (early 1950s) to enhance water quality for CVP exports at Tracy Can pass 6,000 cfs when gates are open, ≈ 20 to 25 percent of Sacramento River flow at Freeport can move into the Mokelumne River Listed salmonids are diverted into the channel when the gates are open. Entrainment rate is related to river flow, time of day, and tidal cycle. Survival of these fish is substantially lower than those fish that remain in the Sacramento River . Early migrating salmon and steelhead (Nov – Jan) are at risk under current operations schedule. The DCC is an artificial channel constructed in the early 50’s to provide high quality Sacramento River water to the Federal pumps at Tracy. It has also been used as a tool to adjust water quality in the western Delta when salinity intrudes into the delta from Suisun Bay. The gates are currently operated primarily during the summer and fall period, closing from February 1 through the end of May to protect outmigrating fish per D Frequently, the gates remain open during the November through January period, closing during high flow events (which are flows > 20 to 25 K cfs) or when triggers are exceeded for Chinook salmon captures at the Knights Landing rotary screw traps or Sacramento area river trawls and beach seines. Several studies have shown that downstream migrating Chinook salmon, and by inference steelhead and green sturgeon, are vulnerable to diversion into the channel when it is open and then subsequently into the Mokelumne River system. Salmonids are much less likely to survive their transit through the interior delta channels than those fish which remain in the mainstem Sacramento River. (Acoustic tagging studies – Vogel, Horn and Blake, Perry and Skalski, Burau et al, and the Delta interior and Delta Action 8 cwt studies Brandes and McLean) Survival is less than one half of the survival in the Sacramento River (0.44) with an average absolute survival rate of approximately 35 percent. Mortality however can even be much higher in any individual study replicate. In addition, when the gates are open, there is a greater probability of fish moving southwards through the central delta to the export facilities (Brandes, McLean 2001, Lowe et al. 2004).

Timing of Juvenile winter-run passage at Knights Landing
rotary screw trap sampling (Low, White, and Chappell 2006) This graphic shows the temporal occurrence of winter-run Chinook juveniles in the late fall and early winter at the Knights Landing Rotary Screw Trap monitoring site. The data indicate that winter-run are present in the lower Sacramento River just upriver from the Delta starting in November. Data from the USFWS monitoring efforts in the lower Sacramento River, and Delta regions indicate that winter-run enter the Delta in December and January and have a continued presence through March. Data from DWR documents indicate that approximately 40 to 45 percent of the annual juvenile winter-run population enters the Delta between November and the end of January.

RPA Overview for DCC Gates
Integrate current monitoring triggers with new gate operations in December and January. Close DCC gates from December 15 to January 31. Weekly evaluations of monitoring data by the Delta Operations for Salmonids and Sturgeon technical team (DOSS). Flexibility of gate operations regarding water quality criteria and experimental studies. Study alternative engineering solutions to control access to the Delta interior The RPA actions for the DCC gate operations builds on the triggers and operations already in place as described in the Salmon Decision Tree Process, but adds new procedures such as the mandatory gate closures starting in mid December to protect downstream migrants. Weekly meetings of the DOSS technical team are held to assess the current monitoring data, including both biological and water quality parameters, DOSS then provides advice to NMFS and the Water Operations Management Team regarding actions to be taken that week. Operational flexibility is built into the RPA actions to allow for specific gate operations regarding water quality issues and the ability to conduct experimental studies in the Sacramento system. For instance, gates can be opened for water quality issues for up to 3 days between December 15 and January 31 during daylight hours at the request of Reclamation or DWR. Gates would be closed at night to protect emigrating fish. Reclamation and DWR would concurrently manage export levels to protect water quality criteria in the Delta. Finally, the RPA has an action to develop alternative engineering solutions to control access of fish to the waterways leading to the Delta interior or to the export facilities which enhance fish survival. An example of this is the recent non-physical barrier tested in the south delta in 2009.

Modeled Changes in Export Levels
CVP and SWP exports increase in both near future (Study 7.1) and future conditions (Study 8.0) compared to the current condition (Study 7.0). Significant increases in exports during the late fall and winter time frames over current operations. SWP exports increase in April and May due to decrease in “fish water” available for export curtailment. In OCAP, the proposed project includes increases in annual export levels as modeled in the CALSim II computer simulations. These increases in exports occur during the months of December, January, and February, at the same time as listed salmonids such as winter-run, yearling spring-run Chinook salmon ,and steelhead smolts are entering the Delta. Additional increases in modeled exports are also seen during April and May when exports are typically reduced for fish protection during the VAMP experiment. The increased exports occur in April and May due to the loss of environmental water to offset export reductions. Previously, the availability of environmental water allowed exports to be reduced outside of the VAMP period, creating shoulders on the VAMP period. 81

Effects to Listed Salmonids
Elevated exports result in an increased potential for entrainment at the export facilities, as well as migrational delays for fish entering the Delta interior, Increases in exports reflected in increased negative Old and Middle River flows Diversion of listed fish into the interior of the Delta increases the risk of mortality (i.e., predation) as well as exposure to contaminants in the Delta interior. Overall mortality in the interior Delta: 35-90% of those that enter the interior Delta 5-20% of winter-run Chinook salmon population entering the Delta San Joaquin River Basin fish have an increased vulnerability to entrainment with increased exports levels. The increased exports are anticipated to increase the risk level of fish emigrating through the Delta either through direct entrainment at the export facilities or by redirecting movements of fish and thus delaying migration through the delta waterways. This applies to fish from the San Joaquin River Basin as well as the Sacramento River basin. Increasing exports creates a larger net negative flow through the waterways of the central and southern delta towards the pumps. The foot print of the pumps influence on the waters of the central and southern delta can be inferred by the magnitude of the OMR flows and the results of particle tracking models. Advection into the central and southern delta waterways results in the loss of a greater percentage of fish either due to predation or other sources, such as contaminants, or eventual entrainment at the pumps. Losses can be as high as 90 percent of the fish entering this region. Any fish leaving the San Joaquin River basin, including the Mokelumne and Calaveras River basins face increased risk of entrainment due to the path these fish must follow through the Delta. Their emigration route runs through the zone of export effects in the main channel of the SJR. 82

Flow Patterns in the Delta
SWP CVP This map illustrates the general zone of influence of the export facilities. The red arrows represent flows from the San Joaquin River basin, the blue arrows from the Sacramento River basin Within the south Delta region, net flows are typically reversed in the delta waterways, and flow towards the CVP and SWP export facilities, the orange shading indicates the general area of the export’s zone of influence. The zone of pumping effects extends out from the export pump location in the southwest corner of the Delta into the waterways of the Delta 83

Projected Old and Middle River Flows
One of the indices I used to assess the impacts of increased exports are the flows in Old and Middle River. These values are from CALSIM II flow data related to exports and river inflows and estimates the net flow of water through the Old and Middle River channels. The more negative the flows, the greater the vulnerability of entrainment is for fish within the Central and Southern Delta waterways. The highlighted cells have OMR flows more negative than cfs, the significance of which will be pointed out in the next series of slides. 84

This graphic shows the locations of the particle injections for the particle tracking model simulations conducted in the Delta. FOCUS ATTENTION ON STATION 815. 85

Particle Entrainment at the Export Facilities under different OMR flows
~ 40% This slide illustrates the potential for entrainment as related to increasing exports. Increased exports are reflected by more negative OMR flows (x – axis). Entrainment potential is related to the percentage of particles entrained (y-axis). This slide also illustrates the effect of proximity to the export facilities on entrainment. Entrainment is greater for injection sites located closer to the exports and occurs at a much faster rate than at sites located farther away. Station 815 is adjacent to the point where the Mokelumne River meets the lower San Joaquin River. Station 902 is near Quimby Island on Old River, while Station 915 is on Old River near Discovery Bay (Orwood Tract), and is the closest station to the exports in this modeling simulation. USFWS 2008

SWP Loss vs. OMR flows Initial Slope
This slide is based on information provided by DWR. It illustrates the non-linear increase in the loss of older salmonids at the State Water Project with increasing exports, represented by the OMR values. More negative OMR values indicate higher export levels and result in much greater losses of fish at the project. CALSIM modeled winter OMR values in December, January, February, and March for the proposed project are more negative than -5,000 cfs and frequently are more negative than -7,000 cfs. The blue shaded region indicates loss which occurs when OMR flows are more negative than cfs, a condition that will frequently occur under the proposed project operations. There are similar relationships between loss and OMR flows at the CVP facilities. 87

RPA Overview for Exports
Integrate current monitoring triggers with new export operations January through June. Limit OMR flows, no more negative than -5,000 cfs January through June. Staged Reductions in exports when fish are present at the facilities, measured by OMR flow levels. Weekly review of operations and fish salvage by the DOSS technical group. Actions compatible with the FWS Delta smelt actions The RPA actions incorporate current fish salvage triggers with new export actions. They utilize the daily monitoring of fish density and salvage numbers that currently occurs to trigger the curtailment of export operations. Exports are managed to keep OMR flows no more negative than -5,000 cfs during the emigration period of listed salmonids. This is a level that is protective of fish as indicated by the loss data presented in the previous graphs. When density or salvage triggers are exceeded, exports are reduced in a staged manner, first to meet an OMR flow target of cfs, and if fish continue to be seen at the facilities, then to an OMR target of -2,500 cfs. Reductions are held for a minimum of 5 days and must have 3 consecutive days where the salvage of fish is below the trigger levels before resuming the normal export levels. This allows fish still currently in the system to move out of the system and away from the pumps influence. The DOSS group will monitor the RPA actions and discuss any changes that may be needed before making recommendations to NMFS and WOMT. This RPA is fully compatible with the FWS actions for Delta smelt and does not preclude actions that they may take.

Direct Entrainment at Project Facilities
Survival is low through the salvage facilities: 1 out of 6 fish survive at the SWP 1 out of 3 fish survive at the CVP Screening Efficiency Predation issues CHTR operations (Collection, Handling, Trucking and Release) Once fish are carried south by the net negative flows, they may survive to be entrained at the export facilities and enter the salvage process. Ultimate survival through these salvage facilities depends on the efficiency of the fish screens, the loss to predation prior to and during salvage, and the eventual release of collected fish back into the system. Estimates of survival, based on numerous studies conducted at the salvage facilities, are very low. At the CVP only 1 out of 3 (35 %) fish survive the salvage process. At the SWP only 1 fish out of 6 survives salvage (16 %). Efficiency of the louvers can be degraded by alterations in flows, removal of louver sections for cleaning (CVP), or gaps or holes in the louvers. In order to increase overall salvage efficiency, the louvers must be kept operating at their design efficiencies or potentially improved. It should be noted that this screening technology is 40 to 60 years old at this time. High losses to predation are present in the salvage process. For example, predation is estimated to be at least 75 percent in Clifton Court Forebay (SWP) and additional predation occurs within the screening and collecting process. The success of releasing salvaged fish back into the San Joaquin River or Sacramento River is hampered by predation that occurs at the point of release. Recent studies have shown that this predation can be significant and that predators cue in on the release process. Improvements to the release strategies are warranted.

Overall survival estimates of fish collection actions
This table presents the methodology for calculating the survival estimates for the 2 fish collection facilities at the SWP and CVP. The different survival factors were derived form studies and reports conducted by the facilities over the past several decades. 90

RPA Overview for Direct Export Entrainment
Increase overall salvage efficiency to 75% for both facilities Directed actions for both facilities include: Improve screening efficiency/operations Reduce predation losses Improve reporting methodology Improve survival of salvaged fish releases Release fish from mobile barges, multiple release sites, or other methods The Overall goal of the RPA action is to improve survival through the salvage process. The RPA target is to get 75 % efficiency as measured by survival at each facility. The RPA calls for specific actions at each facility: Actions are targeted at specific problems identified at each facilities but in general call for better screening efficiency . Lower predation impacts, and the development of more readily accessible salvage and loss data. Improvements to the final release of fish back into the river after salvage. Predators have adapted to the release procedures and congregate around the discharge pipes. Alternative release methods need to be developed and the RPA actions target this.

Indirect Mortality in Delta Interior
Assessed indirect mortality within delta interior utilizing applicable studies and literature. Compared export and non-export related mortality within the interior delta utilizing DWR’s Delta Survival model and CalSim II output from Studies 7.0 (current operations), 7.1 (near future operations), and 8.0 (future operations). Assessed recent survival studies utilizing acoustically tagged fish. An additional element of the project that required assessment was the loss of fish moving across the Delta both due to export related factors as well as “non” export related factors. I used several published reports and as well as agency studies to address this issue. Furthermore, I incorporated the Delta Survival Model developed by DWR to look at the potential levels of loss associated with the proposed exports as represented by the CALSIM modeling efforts for the project. Acoustic tag studies included recent reports by Perry and Skalski, Vogel, and Burau, as well as the series of reports for the VAMP experiments. 92

Results from DWR Survival Model
Monthly export related mortality for Sacramento River fish ranged from <1% to 15% combining all studies and water year types for the period between December and June. Monthly Indirect mortality (non-export) for Sacramento River fish ranged from 3% to 32% combining all studies and water year types for the period between December and June. Higher E/I ratios had higher mortality levels. Higher E/I ratios typically occurred in December and January in drier hydrological conditions. Monthly total population mortality for Sacramento River basin fish migrating downstream in the Sacramento River ranged from 23% to 59% under same conditions as above. This slide summarizes the information generated by DWR’s Delta Survival Model. Based on the data output, fish loss increases with an increasing E/I ratio and will increase in the future under proposed operations which increases pumping levels. There were also seasonal changes based on the export rates. The type of water year also influenced the level of survival and loss due to changes in the export levels. It should be noted that this model is focused on Sacramento River fish, and not on fish entering the Delta from the San Joaquin River system. It is expected that survival levels will be substantially lower in the SJR system as indicated by the findings of the ongoing VAMP experiments. 93

RPA Overview for Indirect Mortality
Indirect mortality is related to most of the project elements associated with the Delta The suite of RPA actions that focus on the Delta elements act in concert to reduce indirect mortality by reducing exposure to the sources of mortality Indirect mortality is that mortality that is not directly associated with actions of the project. This would include predation in the waterways of the delta, advection into waterways leading to the delta interior such as Georgiana Slough, exposure to contaminants, or entrainment into agricultural diversion. However it is clear that project actions can influence the level of indirect mortality experienced by emigrating fish. For example, fish redirected in their movements by net negative flows in the southern delta are exposed to a different level of predators than those that continue on their normal migratory pathway. The suite of RPA actions reduce the direct effects of the project elements, such as closing the DCC gates at the appropriate time or reducing the net negative flows in the Old and Middle River channels, can reduce exposure to sources of indirect mortality.

San Joaquin River Inflow to the Delta
OCAP assumes that VAMP – like flows and exports will continue into the future. BUT: No defined description of this operation has been presented to date and there is limited “fish water” available to offset VAMP water costs in the future. Spring-time flows currently seen during the VAMP operations on the Tuolumne River and Merced River are likely to decline Project and non-project stressors result in 90-99% mortality of Juvenile San Joaquin River steelhead. Increased survival and subsequent adult returns are linked to increased river flows during the juvenile outmigration period The project description for the long term operations of the CVP and SWP (OCAP) did not clearly describe the future operations of the project in the San Joaquin Basin. This vagueness was very problematic for assessing project impacts in this region. The project description indicated that VAMP like flows and export reductions would continue, but did not specify what these actions were going to be. Given the “sunset” of VAMP in the near future, it was considered very likely that flow contributions from the other 2 tributaries would change, thus changing the hydraulics in the lower San Joaquin River main stem and increasing the risk to all salmonids in the basin including listed steelhead. Currently, based on the survival estimates for fall-run Chinook salmon derived during the VAMP studies, the survival rate for San Joaquin River basin steelhead smolts emigrating to the ocean is believed to be very low. This is a result of exposure to numerous stressors associated with both project and non-project sources Historical data and previous studies have shown a consistent trend that increased spring flows result in higher survival rates for emigrating juvenile salmonids and higher adult escapement in subsequent years.

Relationship of April and May flows to Adult Escapement
This graphic represents the adult escapement of fall-run Chinook salmon in the San Joaquin River basin shifted 2.5 years to correspond with spring river flows during their outmigration as juveniles, assuming a 3-year life history periodicity. Fall run are used as a surrogate for the basin’s steelhead population, which is considerably smaller than the fall run populations but require similar water qualities and hydrology for their survival. There is a consistent overlap with higher spring flows and subsequent adult returns.

And Spring Time flows 2.5 years Earlier
Total Escapement to the San Joaquin River Tributaries, 1951 through 1996, And Spring Time flows 2.5 years Earlier This figure shows the spring flow relationship to escapement for fall run in a different format with 95 percent confidence intervals From Baker and Morhardt, 2001

Relationship between Adult Fall-run Chinook Salmon Escapement
and the Vernalis flow to export ratio 2.5 years earlier This graphic illustrates the relationship between the flow/export ratio and the adult escapement 2.5 years later. Adult FR escapement increases with higher flow to export ratios. Thus, increasing spring flows and increasing the flow to export ratio should increase eventual adult escapement in subsequent years for all basin salmonid populations. From 2006 VAMP report 98

RPA Overview for San Joaquin River Flows into the Delta
Flows are based on previous studies and historical gaged flows at Vernalis. Numerous iterations of the proposed flow criteria were run to examine the effects of the action before deciding on a final action. RPA is phased in over time Flexibility in RPA pertaining to water year type and drought conditions Continuing adaptive management Flow criteria were based on historical gaged flows at Vernalis that were present with impaired flows. Flows are substantially less than unimpaired flows. Vernalis flow targets are limited by the availability of only one source of water– the Stanislaus River, that is under the control of Reclamation. Increasing Vernalis flow targets and the duration of the pulse flow window are a reflection of the numerous studies conducted in the watershed to date. Over 40 computer simulations were run with the help of Derek Hilts, USFWS, testing different combinations of input parameters such as reservoir storage indices, water year type, flow to export ratios, drought cycle off ramps, flow targets, etc. The impacts of the RPA action were examined from different perspectives, including reservoir drawdown, water quality goals, export levels, etc. RPA is phased in in 2 parts. The interim San Joaquin River Inflow to Export ratios last 2 year, to allow time for the state water board and FERC processes to augment flows on non federal tributaries. After this 2 year period, the final phase is initiated. The action has inherent flexibility. The San Joaquin flows at Vernalis are tiered to water year types and allows for multiple year drought conditions to trigger an exception procedure to protect human health and safety. A six year study based on the use of acoustically tagged fish is designed to increase our knowledge of factors affecting salmonid survival in the San Joaquin basin and southern Delta. It will look at factors such as flow and export relationships on fish behavior, route selection, reach survival including the tributaries, and overall survival through the Delta. The results of these studies are intended to provide the information necessary to effectively manage the system in an adaptive manner.

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