Summary Matrix of the NMFS and Service Coordinated Long-term Operation BiOps RPA actions

Delta Stewardship Council (Delta Council) | July 1st, 2019

Summary Report on the Transactions of the Smelt Working Group in Water Year 2014

Delta Stewardship Council (Delta Council) | August 29th, 2014

The Bay‐Delta Fish and Wildlife Office (BDFWO) has prepared this report to summarize the implementation the U.S. Fish and Wildlife Service’s (Service) biological opi

The Bay‐Delta Fish and Wildlife Office (BDFWO) has prepared this report to summarize the implementation the U.S. Fish and Wildlife Service’s (Service) biological opinion on the Central Valley Project (CVP) and State Water Project (SWP) Long‐term Operations (BiOp) in Water Year (WY) 2014. In addition to background information pertinent to implementation of the BiOp , this report provides a summary of the transactions of the Smelt Working Group (SWG), as well as water operations and during WY 2014. The SWG is a technical team that evaluates biological and technical issues regarding Delta Smelt (Hypomesus transpacificus) and develops recommendations for consideration by the Service during implementation of the BiOp’s Reasonable and Prudent Alternative (RPA) actions. During WY 2014 the SWG made no recommendations for more restrictive water operations and the Service issued no determinations to reduce water exports.

Summary Report on the Transactions of the Smelt Working Group in Water Year 2018

Delta Stewardship Council (Delta Council) | November 1st, 2018

Summary report: Green sturgeon, longfin smelt, and dredging operations in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | December 1st, 2009

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions f

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions for green sturgeon (Acipenser medirostris Ayres). These changes in the management status, and associated permitting issues, have prompted renewed interest among [long term management strategy] LTMS participants in the management of these native fish. In response, LTMS held symposia on December 2 and 3, 2009, to review and consider the science, management, and policy related to dredging activities and these species. A primary stressor to both species is reduction of appropriate habitat, due to water diversion activities and other basin-scale modifications in water flow. Local studies of dredging have shown little evidence of direct entrainment for either species, and the frequency of encounter with sites of dredging activity is likely to be very low. Nevertheless, spatial and temporal patterns of population movements and reproductive activity vary from year to year, making it difficult to employ an environmental work windows approach. Available information is limited on other direct effects of dredging, including sediment contamination, habitat modification, and underwater noise. Indirect effects due to maintenance of active navigation channels pose potential concerns. In particular, introduction of invasive species, and mortality due to propeller strikes, both warrant attention. As a follow up step to the symposia, we recommend that LTMS host a workshop targeted towards specific LTMS management needs for green sturgeon and longfin smelt. The workshop should include LTMS participants, the scientists that presented at the symposium, and dredging operators, and could focus on the integration of current research findings into tools that would be useful for managers. Appropriate tools for consideration include predictive or descriptive models of species distribution, and of potential impacts of various dredging activities. There should also be consideration of management approaches that broadly address the primary ecosystem-level stressors for green sturgeon and longfin smelt, rather than employing small scale project-level mitigation. In particular, an integrated regional restoration and monitoring program may be the most effective approach to improve the health of the species.

Survey Fishes: An Illustrated List of the Fishes Captured during the Northwest Fisheries Science Center’s Fishery Resource Analysis and Monitoring Division’s West Coast Survey

National Marine Fisheries Service (NMFS) | September 1st, 2017

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM) West Coast surveys. Scientific and technical terms have been kept to a minimum and, when used, are defined within the text. Descriptions and distribution are confined to those species within the geographic (U.S.–Canada to U.S.–Mexico borders) and depth (30–1,680 m) parameters of the FRAM West Coast surveys. Many of the fishes described have geographic and/or depth ranges that extend outside of the survey parameters. Distributions include these areas and are described by political boundaries (e.g., state and/or country borders), bodies of water (i.e., the northeastern Pacific, the Strait of Juan de Fuca, the Columbia River, etc.), islands and/or major geographical features (i.e., the Hawaiian, Farallon, and Channel Islands, Cape Flattery, Point Conception, etc.). Conducted aboard small commercial vessels with limited personnel and space, the majority of the FRAM West Coast surveys do not have access to wet/dry lab facilities for detailed observations. Due to a variety of factors such as body size and specimen damage, internal meristic counts (i.e., vertebrae or pyloric caeca), and others that cannot be made with the naked eye, identification of some groups of fishes included in this text are treated only to the family or generic level. The species accounts are in scientific order as much as possible. The list of common and scientific names are in the List of Species. Photographs are provided when available. The family and species keys are for the families/species within the guide. However, some species not known from within the scope of this work may have been included to complete a couplet.

Synthesizing Relationships Between Winter-Run Chinook Salmon Out-Migration Survival and Water Operations in the Sacramento–San Joaquin Delta

University of California, Davis (UC Davis) | December 19th, 2025

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenil

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenile out-migration through the heavily anthropogenically modified Sacramento–San Joaquin Delta, or Delta. Water exports from pumping facilities in the Delta can alter local hydrology and influence movement of out-migrating juveniles, some of which are observed in or near pumping facilities. Monitoring and regulations, intended to protect out-migrating fish through restrictions on pumping, are predicated on assumed relationships among fish observations, water operations, and through-Delta migratory survival. In this study, we use a new conceptual model to review the current state of science for winter-run Chinook Salmon out-migration survival in the Delta, and use simulation modeling to address pertinent knowledge gaps. Results of this study highlight varying support for the influence of Sacramento River flow, temperature, and water exports on routing and survival in different regions of the Delta. The contributions of specific routing pathways to the interior Delta (e.g., through Threemile Slough) to survival, and the relationship between fish entrainment at pumping facilities and overall migratory survival, remain uncertain. Recommended future work includes continued fine-scale acoustic telemetry studies throughout the Delta, novel integrated modeling of monitoring data, and contextualizing the relevance of Delta-based survival to population viability by incorporating explicit uncertainties about survival into existing life-cycle models.

System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

California Department of Water Resources (DWR) | August 21st, 2017

Senate Bill (SB) X2 1 mandated and allocated resources for “planning and feasibility studies to identify potential options for the reoperation of the state's flood prot

Senate Bill (SB) X2 1 mandated and allocated resources for “planning and feasibility studies to identify potential options for the reoperation of the state's flood protection and water supply systems that will optimize the use of existing facilities and groundwater storage capacity.” Specifically, SB X2 1 stipulated that the studies shall be designed to determine the potential to achieve integration of flood protection and water supply systems to increase water supply reliability and flood protection, improve water quality, and provide for ecosystem protection and restoration. For this evaluation, a suite of ecosystem evaluation metrics were developed to evaluate the effects of reoperation scenarios simulated in Phases II and III of the SRP. Phase II reoperation scenarios were used to develop and test the ecosystem evaluation framework, and to quantify the effects of reoperation at Shasta and Oroville paired with conjunctive use and spring pulse flows. The next step was studying the ecosystem effects of Forecast-Based-Operation (FBO) at Shasta and Oroville combined with conjunctive use and spring pulse flows. Finally, t additional scenarios were developed and evaluated to explore the sensitivity of ecosystem performance to FBO and the potential for reoperation to enhance major ongoing ecosystem restoration efforts in the system. The purpose of this report is to document and describe the methods and results from the ecosystem evaluation to date, and to outline additional steps that could optimize reoperation scenarios for ecosystem improvement. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

Targeting climate diversity in conservation planning to build resilience to climate change

Ecological Society of America (Wiley) | April 24th, 2015

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective g

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real- world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas consistently show greater climate stability than homogenous areas. The analysis suggests that utilizing high-resolution climate and hydrological data in conservation planning improves the likely resilience of biodiversity to climate change. We used these analyses to suggest new conservation priorities for the San Francisco Bay Area.

Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup: Assessment of Aquatic Herbicide Use in the Delta

San Francisco Estuary Institute (SFEI) | May 15th, 2006

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide applications. In this report, the risk quotient calculation method utilized by the Aquatic Pesticide Monitoring Program (a USEPA Tier 1 risk assessment) was used to determine if there are patterns of Level of Concern exceedances that indicate the possibility of adverse impacts on the Delta aquatic ecosystem due to DBW aquatic herbicide applications. Level of Concern exceedances are indicative only of the need for further investigation of an application scenario and do not, in and of themselves, indicate adverse impacts. This type of risk analysis cannot quantify the potential additive or synergistic effects of all pelagic organism stressors (one of which would be aquatic herbicides) within the Delta. This risk assessment indicates that, with the exception of diquat dibromide applications, DBW herbicide applications are unlikely to have the potential to cause Delta ecosystem water quality impacts. While there were a number of Level of Concern exceedances for diquat, DBW and all regulatory agencies involved were aware of this potential prior to application. NOAA Fisheries requested that, when possible, diquat used adjacent to salmon migratory routes should be reduced or avoided when that species is likely to be present. USFWS determined that diquat impact to aquatic invertebrates is minimal, temporary, and not likely to jeopardize Delta smelt but has required avoidance in areas where and when the smelt are known to be present. For 2006, NOAA has allowed DBW to treat sites in April and May with fluridone, which has allowed the use of diquat to be discontinued.

Technologies for Passing Fish at Large Dams

California Department of Water Resources (DWR) | June 1st, 2013

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunit

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunities to provide Central Valley salmonid species access to currently inaccessible habitat (DWR 2008, NMFS 2009, and CA Resources Agency 2009). In addition, Lindley et al. (2007) stated that in order to recover Central Valley salmonids, some populations will need to be established in areas now blocked by dams. “The state should work with dam owners and operators, federal resource management agencies, and other stakeholders to evaluate opportunities to introduce or reintroduce anadromous fish to upper watersheds. Reestablishing anadromous fish, such as salmon, upstream of dams may provide flexibility in providing cold water conditions downstream, and thereby help inform system reoperation.” (CA Resources Agency 2009) The U.S. Bureau of Reclamation dedicates over 1.2 million acre-feet of water, through operation of the Central Valley Project, to fish and wildlife. DWR releases water to meet minimum flow and temperature requirements downstream of Oroville Dam. Climate change may warm rivers and streams, with less water available for ecosystem flow and temperature needs in spring and summer (CA Resources Agency 2009). As temperatures warm, more cold water storage may be needed so that releases can be made to meet temperature requirements downstream. Providing anadromous1 fish passage to areas upstream of reservoirs could eliminate or reduce the need for cold water releases and give water managers additional flexibility in meeting downstream water supply and flood protection needs. In addition, it is prudent to consider fish passage opportunities as part of potential systems reoperations because other agencies are conducting planning efforts for fish passage ...