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Managing Freshwater Discharge to the San Francisco Bay/Sacramento-San Joaquin Delta Estuary―The Scientific Basis for an Estuarine Standard

San Francisco Estuary Project | October 26th, 1992

Summary

Aquatic resources of the Sacramento-San Joaquin Delta and upper portions of San Francisco Bay have undergone significant declines over the past several decades. Species c

Aquatic resources of the Sacramento-San Joaquin Delta and upper portions of San Francisco Bay have undergone significant declines over the past several decades. Species characteristic of the Delta and rivers, such as striped bass and salmon, began to decline during the late 1970s. Prolonged drought, large diversions of fresh water, and dramatic increases in populations of introduced aquatic species during the 1980s and 1990s brought a number of indigenous aquatic species to extremely low levels. Species that spend more of their lives downstream of the Delta, including Delta smelt, longfin smelt, and many zooplankton, maintained large populations through the 1970s, but declined sharply after the mid-1980s. Declines in aquatic resources have led to curtailed fishing seasons, to petitions for endangered species status, and general concern about the health of the estuarine ecosystem.

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Mark/Recapture Experiments at Clifton Court Forebay to Estimate Pre-Screening Loss to Juvenile Fishes: 1976-1993

California Department of Fish and Wildlife (CDFW) | September 30th, 1997

Summary

From October 1976 through November 1993, the California Department of Fish and Game conducted mark/recapture experiments at Clifton Court Forebay, designed to estimate pr

From October 1976 through November 1993, the California Department of Fish and Game conducted mark/recapture experiments at Clifton Court Forebay, designed to estimate pre-screen loss to entrained juvenile fishes. Ten studies were conducted; eight evaluated losses to hatchery-reared juvenile chinook salmon, and two evaluated losses to hatchery-reared juvenile striped bass. Pre-screen loss was calculated from the proportion of marked fish released at the radial gates that were subsequently recaptured during salvage operations at Skinner Fish Facility. The proportion was adjusted for handling mortality, fish facility louver effiCiency, and any subsampling at the facility. Studies were conducted across a wide range of environmental conditions and State Water Project operations, with a wide range in the size ofexperimental fish. Pre-screen loss estimates for juvenile chinook salmon were 63-99%. Potential biases in estimates of pre-screen loss may be due to (1) the calculation for pre-screen loss, (2) underrepresentative and over-representative salvage of experimental fish at Skinner Fish Facility, and (3) the introduction of experimental fish directly into Clifton Court Forebay. A multiple-regression analysis of pre-screen loss to juvenile salmon showed that 91% of the variance in pre-screen loss can be explained by export rate, experimental fish size, and water temperature.

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Methodology for Flow and Salinity Estimates in the Sacramento-San Joaquin Delta and Suisun Marsh

California Department of Water Resources (DWR) | June 1st, 2017

Summary

This is the 38th annual progress report of the California Department of Water Resources’ San Francisco Bay-Delta Evaluation Program, which is carried out by t

This is the 38th annual progress report of the California Department of Water Resources’ San Francisco Bay-Delta Evaluation Program, which is carried out by the Delta Modeling Section. This report is submitted annually by the section to the State Water Resources Control Board pursuant to its Water Right Decision D-1485, Term 9, which is still active pursuant to its Water Right Decision D-1641, Term 8. This report documents progress in the development and enhancement of computer models for the Delta Modeling Section of the Bay-Delta Office. It also reports the latest findings of studies conducted as part of the program. This report was compiled under the direction of Tara Smith, Program Manager for the Bay-Delta Evaluation Program.

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Missing the Boat on Freshwater Fish Conservation in California

Conservation Letters (Society for Conservation Biology) | March 30th, 2016

Summary

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fi

Population growth and increasing water‐use pressures threaten California's freshwater ecosystems and have led many native fishes to the brink of extinction. To guide fish conservation efforts, we provide the first systematic prioritization of river catchments and identify those that disproportionately contribute to fish taxonomic diversity. Using high‐resolution range maps of exceptional quality, we also assess the representation of fish taxa within the state's protected areas and examine the concordance of high‐priority catchments with existing reserves and among distinct taxonomic groups. Although most of the state's native fishes are found within protected areas, only a small proportion of their ranges are represented. Few high‐priority catchments occur within protected areas, suggesting that fish conservation will require active management and targeted river restoration outside of reserves. These results provide the foundation for systematic freshwater conservation planning in California and for prioritizing where limited resources are allocated for fish recovery and protection.

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Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) production in the Sacramento Valley

Ecological Modelling (Elsevier) | March 13th, 2021

Summary

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem h

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.

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National Marine Fisheries Service Biological Opinion for the Long-Term Operations of the Central Valley Project and State Water Project

National Marine Fisheries Service (NMFS) | June 3rd, 2009

Summary

The purpose of this document is to present NOAA’s National Marine Fisheries Service’s (NMFS) biological and conference opinion (Opinion), about whether the U.S. Burea

The purpose of this document is to present NOAA’s National Marine Fisheries Service’s (NMFS) biological and conference opinion (Opinion), about whether the U.S. Bureau of Reclamation’s (Reclamation) proposed long-term operations of the Central Valley Project (CVP), operated in coordination with the State Water Project (SWP; hereafter referred to as CVP/SWP operations, the proposed action, or the project), is likely to jeopardize the continued existence of the following species: Endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha, hereafter referred to as winter-run) Threatened Central Valley spring-run Chinook salmon (O. tshawytscha, hereafter referred to as spring-run) Threatened Central Valley (CV) steelhead (O. mykiss) Threatened Central California Coast (CCC) steelhead (O. mykiss) Threatened Southern Distinct Population Segment (DPS) of North American green sturgeon (Acipenser medirostris, hereafter referred to as Southern DPS of green sturgeon) Endangered Southern Resident killer whales (Orcinus orca, hereafter referred to as Southern Residents) or destroy or adversely modify the designated critical habitat of the above salmon and steelhead species, or proposed critical habitat for Southern DPS of green sturgeon. This Opinion is based on the best scientific and commercial information available.

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Native and alien fishes in a California estuarine marsh: twenty-one years of changing assemblages

American Fisheries Society (AFS) | September 30th, 2002

Summary

We used monthly otter trawling and beach seining to sample the fishes of Suisun Marsh in the San Francisco Estuary from 1979 to 1999. We collected nearly 173,000 fish, mo

We used monthly otter trawling and beach seining to sample the fishes of Suisun Marsh in the San Francisco Estuary from 1979 to 1999. We collected nearly 173,000 fish, mostly young of the year, representing 28 native species and 25 alien species. Catch data were related to temperature, salinity, water transparency, and several measures of freshwater inflow into the marsh. Species abundance and distribution within the marsh were the product of several interacting factors: (1) the timing and place of reproduction of the abundant resident species, (2) past reproductive success, (3) habitat differences among sloughs, and (4) physiological tolerance. We did not find consistent groups of potentially interacting species, although some native species showed weak concordance in abundance. The lack of persistent fish assemblages is related to the naturally fluctuating environmental conditions of the estuary, the overall decline in fish abundance through time, and the frequent invasions of alien fishes and invertebrates. Our results suggest that the fish assemblages in Suisun Marsh will continue to be unpredictable until estuarine processes approach their historic range of variability and alien invasions are halted.

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Natural Resources Defense Council v. Kempthorne, Order Granting in Part and Denying in Part Plaintiffs’ Motion for Summary Judgment

United States District Court, Eastern District of California | May 7th, 2007

Summary

This case concerns the effect on a threatened species of fish, the Delta smelt (Hypomesus transpacificus) , of the coordinated operation of the federally managed Central

This case concerns the effect on a threatened species of fish, the Delta smelt (Hypomesus transpacificus) , of the coordinated operation of the federally managed Central Valley Project ("CVP") and the State of California's State Water Project *2 ("SWP"), among the world's largest water diversion projects. Both projects divert large volumes of water from the California Bay (Sacramento - San Joaquin) Delta ("Delta") and use the Delta to store water.

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North Coast Regional Water Quality Control Board Fact Sheet

California State Water Resources Control Board (SWRCB) | March 1st, 2010

Summary

The North Coast Region receives more precipitation than any other part of California. Abundant in surface water and groundwater resources, the North Coast Regio

The North Coast Region receives more precipitation than any other part of California. Abundant in surface water and groundwater resources, the North Coast Region constitutes only about 12 percent of the area of California but produces about 40 percent of the annual runoff. Encompassing some 19,390 square miles, including 340 miles of coastline and remote wilderness, urban and agricultural areas, the North Coast Region is divided into two natural drainage basins—the Klamath River Basin and the North Coastal Basin.

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North Delta Water Management Program

California Department of Water Resources (DWR) | March 1st, 1988

Summary

Water management issues surrounding the Sacramento-San Joaquin Delta continue to challenge water resource planners in California. Many agree there are problems and urge

Water management issues surrounding the Sacramento-San Joaquin Delta continue to challenge water resource planners in California. Many agree there are problems and urge that they be corrected, but a consensus on how best to solve them has not yet been reached. Problems include frequent flooding due to unstable levees and constricted channels, flow patterns that are unfavorable for fish and water quality, and water level and circulation patterns that hinder irrigation. During the last several years, various water resources problems have been corrected through application of the public environmental documentation and regulatory permit process. This process has also shown the importance of Federal permit regulations in governing projects in the Delta estuary. To facilitate planning, the estuary has been divided into three study areas for evaluation of problems and needs unique to each area -- North, South, and West. This report discusses concepts for a North Delta Water Management Program. The long-term planning and environmental documentation process will includeother reports and will take about three years to complete. Planning flexibility afforded by the environmental documentation and regulatory permit process is expected to allow many of the concerns surrounding Delta water management to be resolved.

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