Letter from National Marine Fisheries Service: Re: Proposed Modification to the Annual Review Schedule Required as Part of the Reasonable and Prudent Alternative in the National Marine Fisheries Service’s 2009 Biological Opinion on the Coordinated Long-term Operation of the Central Valley Project and State Water Project (June 30, 2016)

Delta Stewardship Council (Delta Council) | June 30th, 2016

Letter from U.S. Bureau of Reclamation: Proposed Modification to the Annual Review Schedule Required as Part of the Reasonable and Prudent Alternative in the National Marine Fisheries Service’s 2009 Biological Opinion on the Coordinated Long-term Operation of the Central Valley Project and State Water Project (April 25, 2016)

Delta Stewardship Council (Delta Council) | April 25th, 2016

Listen to the River: An Independent Review of the CVPIA Fisheries Program

U.S. Bureau of Reclamation (USBR) | December 12th, 2008

In 1992 Congress directed the Department of Interior to develop and implement a program that makes “all reasonable efforts” to ensure and sustain on a long-term basis

In 1992 Congress directed the Department of Interior to develop and implement a program that makes “all reasonable efforts” to ensure and sustain on a long-term basis a doubling of the number of naturally produced anadromous fish in Central Valley rivers and streams by 2002. Doubling did not happen by the legislative goal of 2002, or by 2008, nor is it likely to ever occur unless renewed commitments and improvements are made to the CVPIA program. The specific “doubling” mission itself may make little scientific or policy sense, especially within the time frames demanded. Yet it is also far from clear that the agencies have done what is possible and necessary to improve freshwater conditions to help these species weather environmental variability, halt their decline and begin rebuilding in a sustainable way. A number of the most serious impediments to survival and recovery are not being effectively addressed, especially in terms of the overall design and operation of the Central Valley Project system. Underlying this independent review of the CVPIA anadromous fish program, asked for by the federal agencies, is the question why the CVPIA program has not been successful in achieving its mission. In this report, we identify scientific, institutional and programmatic obstacles to the success of the CVPIA, drawing conclusions from the information provided. Based on these conclusions, we make recommendations to Reclamation and the Service on how these obstacles might be overcome.

Local hydraulics influence habitat selection and swimming behavior in adult California Central Valley Chinook salmon at a large river confluence

Fisheries Research (Elsevier) | February 2nd, 2023

Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | June 30th, 2008

Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of

Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of salvage counts with population indices have failed to provide quantitative estimates of the magnitude of this mortality. I estimated the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) to place these losses in a population context. The estimate for salmon was based on recoveries of tagged smolts released in the upper Sacramento River basin, and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta. The proportion of fish salvaged increased with export flow, with a mean value around 10% at the highest export flows recorded. Mortality was around 10% if pre-salvage losses were about 80%, but this value is nearly unconstrained. Losses of adult delta smelt in winter and young delta smelt in spring were estimated from salvage data (adults) corrected for estimated pre-salvage survival, or from trawl data in the southern Delta (young). These losses were divided by population size and accumulated over the respective seasons. Losses of adult delta smelt were 1–50% (median 15%) although the highest value may have been biased upward. Daily losses of larvae and juveniles were 0–8%, and seasonal losses accumulated were 0–25% (median 13%). The effect of these losses on population abundance was obscured by subsequent 50-fold variability in survival from summer to fall.

Lower Mill Creek Watershed Conjunctive Use Project: Tehama County, California

California Department of Water Resources (DWR) | November 18th, 2008

In 1920, the Tehama County Superior Court of the State of California adjudicated entitlements to all Mill Creek flow below 203 cubic feet per second (cfs). As such, water

In 1920, the Tehama County Superior Court of the State of California adjudicated entitlements to all Mill Creek flow below 203 cubic feet per second (cfs). As such, water right holders on Mill Creek legally divert a significant portion of the surface water flow for agricultural beneficial use. During certain times of the year, especially during dry or critically dry years, the agricultural demand for surface water can reduce Mill Creek flow and expose in-stream barriers to fish migration. Fishery experts recognize Mill Creek as a high priority stream for the protection and enhancement of Chinook salmon spawning habitat. Mill Creek surface water diverters currently participate in a long-term cooperative management plan to help provide sufficient flow for fish migration while also maintaining irrigation supplies and the recognition of surface water rights. As part of these efforts, Mill Creek water users participate in water lease and groundwater exchange programs designed to increase in-stream flow during critical spring and fall fish migration periods. Along with other entities, the Department of Water Resources (DWR) plans to establish methods of monitoring and studying fish passage, assessing agricultural water use efficiency, and examining the potential for additional use of groundwater as opposed to use of surface water diversions in the Lower Mill Creek watershed. This report provides a background of the geology and hydrogeology in the Lower Mill Creek watershed area, a detailed discussion of the groundwater resources, and an overview of the potential for conjunctive use of surface water and groundwater resources. It also provides recommendations for additional groundwater monitoring and potentially favorable locations for production well installation associated with possible future conjunctive use programs.

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

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.

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

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. 

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

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

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.

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

California Department of Water Resources (DWR) | December 1st, 2019

Various water resource management actions have been planned to protect and restore salmon populations for a healthy Sacramento-San Joaquin Delta (Delta) ecosystem. Curren

Various water resource management actions have been planned to protect and restore salmon populations for a healthy Sacramento-San Joaquin Delta (Delta) ecosystem. Currently, evaluating the effectiveness of these actions relies on field studies and/or expert opinion. Field studies can be costly and may not provide a comprehensive assessment for a range of applications because of limited study areas, durations, and river conditions. Expert opinion, although valuable, may under- or over-emphasize the importance of certain project components.  To supplement field studies and provide a quantitative assessment tool, the California Department of Water Resources (DWR), in collaboration with the United States Geological Survey (USGS), developed an ecological modeling tool, ECO-PTM. ECO-PTM is an individual-based juvenile salmon migration model that is based on a random-walk particle-tracking method with fish-like behaviors attached to the particles. The behavioral parameters are estimated from acoustic telemetry tag data of juvenile late-fall Chinook salmon (Tag Data) from various field studies (Perry et al. 2018). A stochastic optimization tool, Particle Swarm Optimization, is used to calibrate the swimming behavior parameters. ECO-PTM can simulate juvenile salmonid migration timing, routing, and survival.  This chapter describes ECO-PTM and its behavioral modules, and the model performance and applications to assist water resource management planning, assessment, and decision-making related to juvenile salmonid survival outcomes.