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.

Systematic Screening of Dams for Environmental Flow Assessment and Implementation

Oxford University Press (OUP) | November 30th, 2014

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.

Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

The Collapse of Pelagic Fishes in the Upper San Francisco Estuary: El Colapso de los Peces Pelagicos en La Cabecera Del Estuario San Francisco

American Fisheries Society (AFS) | January 9th, 2007

Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of res

Although the pelagic fish community of the upper San Francisco Estuary historically has shown substantial variability, a recent collapse has captured the attention of resource managers, scientists, legislators, and the general public. The ecological and management consequences of the decline are most serious for delta smelt (Hypomesus transpacificus), a threatened species whose narrow range overlaps with large water diversions that supply water to over 25 million people. The decline occurred despite recent moderate hydrology, which typically results in at least modest recruitment, and investments of hundreds of millions of dollars in habitat restoration and environmental water allocations to support native fishes. In response to the pelagic fish collapse, an ambitious multi-agency research team has been working since 2005 to evaluate the causes of the decline, which likely include a combination of factors: stock-recruitment effects, a decline in habitat quality, increased mortality rates, and reduced food availability due to invasive species.

The Decline of Striped Bass in the Sacramento-San Joaquin Estuary, California

American Fisheries Society (AFS) | July 1st, 1985

The abundance of young striped bass Morone saxatilis in the Sacramento-San Joaquin Estuary has suffered an unsteady but persistent decline from population levels that wer

The abundance of young striped bass Morone saxatilis in the Sacramento-San Joaquin Estuary has suffered an unsteady but persistent decline from population levels that were high in the middle 1960s. The decline was particularly severe in 1977 and abundance of young striped bass has been low every subsequent year. The adult striped bass population also has fallen during the past 20 years, but the exact period over which the decline occurred and the rate of decline are not clear. The adult population is now about one-quarter of its former size and there is little sign of recovery. We believe the Sacramento-San Joaquin striped bass population and the fishery that it supports are in serious danger. The cause is most likely one or more of four factors. (1) The adult population is now so low that egg production may be inadequate. (2) The plankton food supply of young striped bass in the western Sacramento-San Joaquin Delta and Suisun Bay has been greatly reduced each spring. Diversion of water from the delta for agricultural purposes is a prime suspect for the decrease in food production. (3) Large numbers of young fish are lost by entrainment in water diversions. (4) The population is stressed by toxic substances such as petrochemicals and pesticides. Additional studies are underway to help determine the principal cause(s) of the striped bass decline.

The Delta Plan: Ensuring a reliable water supply for California, a healthy Delta ecosystem, and a place of enduring value

Delta Stewardship Council (Delta Council) | May 16th, 2013

The Sacramento-San Joaquin River Delta is the grand confluence of California’s waters, the place where the state’s largest rivers merge in a web of channels—and in

The Sacramento-San Joaquin River Delta is the grand confluence of California’s waters, the place where the state’s largest rivers merge in a web of channels—and in a maze of controversy. The Delta is a zone where the wants of a modern society come into collision with each other and with the stubborn limitations of a natural system. In 2009, seeking an end to decades of conflict over water, the Legislature established the Delta Stewardship Council with a mandate to resolve long-standing issues. The first step toward that resolution is the document you have before you, the Delta Plan.

The Effects of Salmon Fisheries on Southern Resident Killer Whales

National Marine Fisheries Service (NMFS) | November 30th, 2012

The Influence of Zooplankton Availability on Delta Smelt Condition and Foraging Across Habitat Contexts

Publisher not available | December 19th, 2025

Strategies for endangered species conservation may have different outcomes depending on the habitat context in which they are implemented. Understanding these context-dep

Strategies for endangered species conservation may have different outcomes depending on the habitat context in which they are implemented. Understanding these context-dependent effects can help optimize and target management efforts. In this analysis, we investigate how environmental and food-web conditions interactively affect condition and foraging of Delta Smelt (Hypomesus transpacificus), an endangered fish endemic to the San Francisco Estuary (the estuary). Food limitation, in terms of pelagic zooplankton availability, is considered a main factor that contributes to the decline in Delta Smelt abundance. Our overarching objective was to examine whether the effect of zooplankton on Delta Smelt depended on habitat context. Specifically, we hypothesized that zooplankton would less positively effect Delta Smelt condition—as measured by hepatosomatic index (HSI)—and foraging success in areas with nearby tidal wetlands, because these adjacent habitats may provide access to prey items from the epibenthos and fringing vegetation. In contrast, in regions with limited proximity to wetlands, we hypothesized that Delta Smelt would rely more on pelagic prey, which would manifest as a more positive effect of zooplankton on body condition and foraging success for Delta Smelt. Using models that accounted for habitat in multiple ways, we found little evidence that zooplankton and habitat interactively influenced Delta Smelt condition or gut fullness. Rather, the influence of zooplankton on HSI and gut fullness was generally positive across habitat contexts. Given the well-documented food limitation in the estuary, promoting the availability of pelagic zooplankton is a rational, albeit complex, management aim. Furthermore, our results suggest that efforts to increase zooplankton would broadly benefit Delta Smelt across a wide range of habitat contexts.

The Klamath River’s dams are being removed. Inside the effort to restore a scarred watershed

Los Angeles Times | March 24th, 2024

HORNBROOK, Calif. — Near the California-Oregon border, reservoirs that once submerged valleys have been drained, revealing a stark landscape that had been underwater fo

HORNBROOK, Calif. — Near the California-Oregon border, reservoirs that once submerged valleys have been drained, revealing a stark landscape that had been underwater for generations. A thick layer of muddy sediment covers the sloping ground, where workers have been scattering seeds and leaving meandering trails of footprints. In the cracked mud, seeds are sprouting and tiny green shoots are appearing. With water passing freely through tunnels in three dams, the Klamath River has returned to its ancient channel and is flowing unhindered for the first time in more than a century through miles of waterlogged lands.