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  • Title

    Delta Salmon Rearing Project

    Lead San Francisco Estuary Institute [SFEI]
    Description This project summarizes existing research and knowledge around suitable rearing habitat for Chinook salmon in the Sacramento-San Joaquin Delta;identifies areas of suitability for rearing salmon using a combined suitability analysis of four mapped habitat parameters;and provides recommendations for types of restoration needed to improve or restore rearing habitat, as well as to identify where in the Delta these restoration efforts could be prioritized.
    Science topics Salmon rearing, Salmon migration, Habitat restoration
    Updated April 29, 2022
  • Title

    Yolo Bypass Salmonid Habitat Restoration and Fish Passage

    Lead California Department of Water Resource [DWR]
    Description The Yolo Bypass Salmonid Habitat Restoration Project works to reconnect the floodplain for fish during the winter season and improve connectivity within the bypass and to the Sacramento River. The project provides seasonal inundation that mimics the natural process of the Yolo Bypass floodplain and improves connectivity within the bypass and to the Sacramento River.
    Science topics Chinook Salmon, Endangered species, Green sturgeon, Habitat restoration, Salmon migration, Salmon rearing, Steelhead Trout, Sturgeon, White Sturgeon
    Updated July 22, 2024
  • Title

    A Next-generation Model of Juvenile Salmon Migration through the Sacramento-San Joaquin Delta

    Lead University of California - Santa Cruz [UCSC]
    Description While migrating through the Delta and its tributaries, Chinook salmon and steelhead move through diverse habitats, encounter predators, interact with highly dynamic flows, and are impacted by a multitude of human-made structures. Funding for this Project will be use to develop integrated system-level models that will effectively manage salmonid populations and other key resources in the California Central Valley.
    Science topics Salmon migration
    Updated November 18, 2022
  • Title

    Quantifying the contribution of tidal flow variations to survival of juvenile Chinook salmon

    Lead U.S. Geological Survey [USGS]
    Description The purpose of this project is to quantify how tides in the Delta influence survival of juvenile salmon. Juvenile salmon survival increases when there is more flow and the river is less tidally influenced. We hypothesize that the increase in survival is because of reduced travel times causing less exposure to predators. This project will test this hypothesis using multiple models including ones that can predict how management actions that modify tidal patterns affect juvenile salmon survival.
    Science topics Chinook Salmon, Salmon migration, Surface water flow, Tides, Water management
    Updated June 17, 2024
  • Title

    Synchrony of Native Fish Movements: Synthesis Science Towards Adaptive Water Management in the Central Valley (FishSync)

    Lead University of California - Davis [UC Davis]
    Description Salmon and other native California fishes are in decline and increasingly targeted for enhanced conservation. Acoustic telemetry technologies have emerged, allowing researchers to track fish routes through the Central Valley. Yet while the use of acoustic telemetry has widened, little synthesis has occurred on the large, growing, and expensive datasets that already exist. The main goal of the project is to conduct a synthesis study of existing and high priority telemetry datasets for native and non-native fishes in the Central Valley. Using synchrony of movement rates, through space and time, we will develop a novel behavior-based statistical framework to gain understanding into the environmental conditions that promote movement/passage of diverse native fishes in the Central Valley. The project includes a Technical Advisory Group, composed of members of multiple conservation teams. The group will inform each step of study, strengthen syntheses, and enable rapid communication of results to decision makers. In total, the project will analyze 10 to 15 high-quality telemetry datasets encompassing a range of native fishes and life stages. This synthesis will yield major insights into water management practices that could help improve survival of native fish. (Green sturgeon image is a CDFW photo, taken by Mike Healy. Source: https://californiawaterblog.com/2023/02/12/green-sturgeon-in-california-hidden-lives-revealed-from-long-term-tracking/)
    Science topics Chinook Salmon, Fish, Salmon migration, Steelhead Trout, Sturgeon, White Sturgeon
    Updated March 9, 2026
  • Title

    Enhanced Acoustic Tagging, Analysis, and Real-Time Monitoring

    Lead National Oceanic and Atmospheric Administration [NOAA]
    Description

    This project tracks the movement and survival of wild and hatchery juvenile Chinook salmon with a large acoustic receiver network (JSATS), including real-time receivers, and the development of real-time metrics and retrospective modeling of juvenile salmon migration data. Need There is a well-documented need for improved detection and associated modeling of salmon migration and survival in the Central Valley. Understanding salmon survival and movement dynamics in the Delta and its tributaries is critical to the operation of state and federal water projects, recovery of ESA-listed species, and sport and commercial fisheries management. Objectives: Maintain 20 real-time JSATS receivers: will provide information on migrating salmon smolt location and timing of Delta entry and exist, which is key for informing time-sensitive decisions; Deployment of autonomous JSATS receiver array: this will provide fine-scale reach-specific survival and movement rates; Development of new metrics for the real-time data: this will inform key management relevant questions, such how many fish are entrained at critical junctions; Development of real-time website to convey movement and survival rates of acoustic tagged juvenile salmonids at various real-time locations in the Sacramento River and Delta.
    Science topics Salmon migration
    Updated February 8, 2026
  • Title

    Delta Juvenile Fish Monitoring Program [DJFMP]

    Lead U.S. Fish and Wildlife Service [USFWS]
    Description

    The Delta Juvenile Fish Monitoring Program (DJFMP) has monitored natural-origin and hatchery-origin juvenile Chinook Salmon (Oncorhynchus tshawytscha) and other fish species within the San Francisco Estuary (SFE) since 1976 using a combination of midwater trawls and beach seines. Since 2000, three trawl sites and at least 58 beach seine sites have been sampled weekly or biweekly within the SFE and lower Sacramento and San Joaquin Rivers. The main objectives of the DJFMP are:
    1. Document the long-term abundance and distribution of juvenile Chinook Salmon in the Delta.
    2. Comprehensively monitor throughout the year to document the presence of all races of juvenile Chinook Salmon.
    3. Intensively monitor juvenile Chinook salmon during the fall and winter months for use in managing water project operations (Delta Cross Channel gates and water export levels) on a real-time basis.
    4. Document the abundance and distribution of Steelhead.
    5. Document the abundance and distribution of non-salmonid species.

     
    Science topics Aquatic vegetation, Chinook Salmon, Conductivity, Crustaceans, Dissolved oxygen, Endangered species, Environmental drivers, Estuaries, Fish, Habitat, Historical ecology, Intertidal and transition zones, Invasive and non native species, Invertebrates, Jellyfish, Main channels, Monitoring methods and techniques, Mysis, Open water, Other species, Pelagic fish, Salinity, Salmon migration, Salmon rearing, SAV and FAV, Steelhead Trout, Turbidity, Water conveyance and infrastructure, Water management, Water operations and exports, Water temperature
    Updated May 21, 2025
  • Title

    Yolo Bypass Fish Monitoring

    Lead California Department of Water Resource [DWR]
    Description California Department of Water Resources (DWR) has operated a fisheries monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: (1) collect baseline data on lower trophic levels (phytoplankton, zooplankton, and aquatic insects), juvenile fish and adult fish, hydrology, and water quality parameters;(2) investigation of the temporal and seasonal patterns in chlorophyll-a concentrations, including whether high concentrations are exported from the Bypass during agricultural and natural flow events and the possibility of manipulating bypass flows to benefit listed species like Delta Smelt (Hypomesus transpacificus) and Chinook salmon (Oncorhynchus tshawytscha). The YBFMP operates a rotary screw trap and fyke trap, and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts.
    Science topics Chinook Salmon, Chlorophyll A B, Conductivity, Delta Smelt, Direction, Dissolved oxygen, Endangered species, Fish, Flood, Food webs, Green sturgeon, Habitat, Habitat restoration, Insects, Intertidal and transition zones, Invasive and non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen and ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater and freshwater marshes, SAV and FAV, Seasonally flooded, Solar irradiance, Stage, Steelhead Trout, Striped bass, Sturgeon, Submerged aquatic vegetation, Surface water flow, Tides, Turbidity, Velocity, Water, Water temperature, Wetlands, White Sturgeon, Zooplankton
    Updated August 28, 2024
  • Title

    Non-Invasive Environmental DNA Monitoring to Support Tidal Wetland Restoration

    Lead University of California - Davis [UC Davis]
    Description In this project we use single-species and multi-species environmental DNA (eDNA) approaches to monitor tidal wetland restoration sites and paired reference sites (existing, unrestored tidal wetlands located near restoration sites) in the San Francisco Bay Delta (SFBD). We are working in coordination with the CDFW Fish Restoration Program (FRP) and other collaborators so our eDNA detections can be paired with physical detections of fishes from their trawling efforts. Ultra-sensitive DNA single species detection methods are being used to identify restoration site use by listed species (Delta Smelt, Longfin Smelt, winter- and spring-run Chinook Salmon) while the DNA metabarcoding approach will evaluate entire fish communities (groups of different fish species) at restored and reference sites. Aside from revealing restored habitat use by other fishes, metabarcoding will reveal potential ecological interactions between Endangered Species Act listed and non-listed species, through concurrent detection in time and space. Sampling throughout the year will allow us to identify seasonal trends in fish use of restored and reference sites. This project will demonstrate the utility of eDNA detection as a non-invasive (no take), cost-effective monitoring tool that can complement conventional surveys of restored tidal wetlands in the SFBD. Our results can be incorporated into an adaptive monitoring framework for tidal wetland restoration, to increase success of future restoration projects.
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Estuaries, Fish, Green sturgeon, Habitat, Habitat restoration, Invasive and non native species, Invertebrates, Longfin Smelt, Mollusks, Pelagic fish, Restoration, Restoration planning, Sacramento Splittail, Salmon migration, Salmon rearing, Steelhead Trout, Striped bass, Sturgeon, Tidal wetlands, Wetlands, White Sturgeon
    Updated May 24, 2024
  • Title

    Open-Source Resources for the Sacramento-San Joaquin Delta Telemetry Research Community

    Lead Cramer Fish Sciences
    Description There is a great deal of telemetry data amassed from studies in the Sacramento-San Joaquin Delta. It continues to grow every year with special studies and monitoring efforts. Multiple research priorities surrounding fish ecology in the Delta could be addressed, at least in part, by synthesizing the myriad telemetry data sets that exist; this work would benefit greatly from the centralization and standardization of data workflows surrounding telemetry research. With the guidance of a PIT Advisory Team, we plan to establish a collection of open-source, technology-agnostic, accessible resources to support a reproducible and transparent telemetry data workflow for researchers in the region. The workflow and resources do not invent new procedures, rather improve and standardize those already used by the telemetry research community. This will bring us in closer alignment with centralized, coordinated data workflows that have been successfully implemented in other regions and data communities. The final open-source set of resources will include a design and roadmap for implementing a central telemetry database and workflow, an R package for the preparation, QA/QC, and basic analysis of telemetry data, and a regional workshop offering training programs in the proposed telemetry data workflow.
    Science topics Chinook Salmon, Fish, Other species, Salmon migration, Steelhead Trout, Striped bass, Sturgeon
    Updated August 26, 2024
  • Title

    Standard Operating Procedure for Diagnosing and Addressing Predator Detections in Salmon Telemetry Data

    Lead University of Washington [UW]
    Description Tag predation is a complicating factor in juvenile salmon telemetry studies that can bias results, delay timely reporting, and prevent effective data synthesis. This project addresses the problem by (1) characterizing predatory fish movement patterns from existing telemetry data in the Delta; (2) developing a standard operating procedure for diagnosing and handling detections of predated tags in salmon telemetry studies; and (3) implementing the recommendations in a software package in Program R that includes code, a “library” of expected predator behaviors, and example vignettes. The R package will be freely available for download at www.cbr.washington.edu.
    Science topics Chinook Salmon, Endangered species, Fish, Intertidal and transition zones, Invasive and non native species, Predation, Salmon migration, Steelhead Trout, Striped bass
    Updated April 30, 2025
  • Title

    Impacts of predation and habitat on Central Valley Chinook smolt survival

    Lead University of Vermont, USGS Vermont Cooperative Fish and Wildlife Research Unit
    Description The Sacramento River in California’s Central Valley has been highly modified over the past 150 years due to mining, urbanization, and impoundment/diversion of river flow to provide water for municipal, industrial, and agricultural needs. Land use changes combined with high levels of harvest have been accompanied by drastic declines in native salmon populations, including the once abundant Chinook salmon (Oncorhynchus tshawytscha). Further, the region has been subject to the introduction and widespread establishment of non-native fish species, some of which are predators of juvenile salmon. Of the four historic ecotypes of Chinook salmon (fall, late-fall, winter, and spring runs), winter- and spring-runs have been most impacted and are currently listed as endangered and threatened respectively under the US Endangered Species act. Past research has illustrated how smoltification of juvenile salmon and outmigration from freshwater to the ocean is a time of increased mortality, and reduced survival at this life stage can impact the number of reproducing adults returning to the system in subsequent years. While these studies have provided valuable information on how habitat and environmental conditions experienced by migrating Chinook salmon smolts can affect survival, they have primarily focused on individual ecotypes during the portion of the year where downstream migrations occur. However, variation in smolt size and migration timing among ecotypes can expose migrating fish to differing environmental conditions and levels of exposure to predation, which can present distinct risks for outmigration survival. To identify the areas and environmental conditions which have the greatest relative impact on juvenile survival for each ecotype, this project will use over ten years of data (2012-2022) from acoustically tagged smolts representing all four Chinook salmon ecotypes in the Sacramento River/Central Valley. Combining these data will increase sample size relative to previous studies, the range of environmental conditions (e.g., temperature, flow, and predator abundance) modeled, the range of fish sizes, and thus, the statistical power of our analyses. We hypothesize that each ecotype will have different factors that will be the primary drivers of mortality experienced during outmigration. To test our hypotheses, we will implement Cormack-Jolly-Seber (CJS) mark-recapture models to estimate both the probability of survival through reaches of the Sacramento River delineated by acoustic receivers, and the detection probability in each reach. Survival will be modeled as a function of individual, release group, reach-specific, and time-varying covariates. Further, to examine the relative impact of predation on smolt survival, we will include an additional covariate representing predator-prey encounter rates using the Mean Free-path Length model. Finally, model selection will be applied to a series of CJS models to assess the relative impact of each covariate on smolt survival for each of the four Chinook ecotypes.
    Science topics Chinook Salmon, Environmental drivers, Fish, Flows, Habitat, Predation, Salmon migration, Water temperature
    Updated February 2, 2024
  • Title

    Development and maintenance of SacPAS website and research for management of Central Valley salmon and other fish species

    Lead University of Washington [UW]
    Description

    SacPAS serves to provide information integration services to the Central Valley Project Improvement Act and practitioners working on matters related to ESA-listed fishes. The web-based services relate fish passage to environmental conditions and provide resources for evaluating the effects of river management and environmental conditions on salmon passage and survival.

    The work performed as part of this agreement includes developing, maintaining, and making accessible query tools and decision support tools to access: historical, real-time and forecasted data; data summaries and visualizations; and hindcasts, forecasts, and scenario-derived predictions from statistical and mechanistic models. More specifically, the objectives are to: 

    1)    Maintain and extend a secondary data repository of historical, real-time, and forecasted fish, environmental, and operational data from the Sacramento River and other river systems in the Central Valley, integrated from primary, public databases. 

    2)    Maintain and improve the data query and visualization tools and services provided through the SacPAS website (https://www.cbr.washington.edu/sacramento/) for historical, real-time, and forecasted environmental and fish data.

    3)    Conduct research and provide access to modeling tools for fish survival and migration, through the SacPAS website, in support of Reclamation-funded and ESA-mandated activities, especially in efforts to predict, track, and evaluate the efficacy of proposed or actual actions.
     
    Science topics Chinook Salmon, Delta Smelt, Endangered species, Environmental drivers, Fish, Flows, Green sturgeon, Longfin Smelt, Salmon migration, Stage, Steelhead Trout, Sturgeon, Temperature, Velocity, Water, Water intakes and fish screens and passage, Water management, Water operations and exports, Water storage, Water temperature, White Sturgeon
    Updated March 8, 2026
  • Title

    Applying a response spectrum model to assess spatial and temporal differences in effects of pesticide mixtures on juvenile Chinook Salmon in the Delta

    Lead University of California - Davis [UC Davis]
    Description

    Pesticide mixtures originating from both legacy and current-use chemicals are widely detected in Delta waters, sediments, and invertebrate prey, posing potential risks to juvenile Chinook Salmon during critical rearing periods. While pesticides have been measured in juvenile salmon and their prey, substantial uncertainty remains regarding how mixtures of contaminants affect fish behavior and physiology, and how these effects vary across space and time within the Delta. This science activity will apply a recently developed response spectrum modeling framework to evaluate spatial and temporal patterns of sublethal pesticide effects on juvenile Chinook Salmon rearing in the Delta. The model integrates pesticide concentrations measured in salmon tissues to predict behavioral and physiological impairment associated with complex pesticide mixtures. Juvenile fall-run Chinook Salmon collected through existing Delta monitoring programs, including archived specimens from prior years, will be analyzed alongside hatchery-origin juveniles deployed in cages at multiple Delta locations. This combined approach will allow assessment of how pesticide bioaccumulation and model-predicted effects vary across habitats, seasons, and hydrologic conditions. Results will provide a predictive assessment of where and when pesticide mixtures are most likely to impair juvenile salmon performance, with implications for growth, survival, and population-level outcomes. The activity will support management decisions related to pesticide regulation, TMDL development, and evaluation of habitat restoration actions, including reconnected floodplain rearing habitats. In addition, spatial patterns of pesticide bioaccumulation may help identify contaminant sources and inform targeted remediation strategies.
    Science topics Bioaccumulation, Chinook Salmon, Endangered species, Fish, Habitat, Insecticides, Pesticides, Salmon migration, Toxicity
    Updated January 9, 2026
  • Title

    Estimating Juvenile Production and Run Timing of Spring Chinook Salmon Leaving the Delta

    Lead U.S. Geological Survey [USGS]
    Description

    Spring-run Chinook salmon (Oncorhynchus tshawytscha) are a high-priority species under the Endangered Species Act due to their risk of extinction. However, understanding the factors affecting their populations is difficult when monitoring focuses only on returning adult spawners. This limited view overlooks critical life stages. To address this gap, the project aimed to estimate the number of juvenile salmon leaving the Delta at Chipps Island. Monitoring salmon throughout their entire life cycle is essential for identifying the key factors influencing their survival and reproduction.

    There is a need from both scientists and managers for accurate data to make informed decisions about salmon protection and conservation. The Department of Water Resources (DWR) mandates that juvenile production estimates for spring-run salmon be included in their incidental take permit, which is necessary for the continued operation of the State Water Project. A method to estimate juvenile abundance of spring-run salmon leaving the Delta (at Chipps Island) did not yet exist.

    To develop these annual estimates, researchers built on previous studies and incorporated new genetic data into updated models. This approach maximized the use of available information and the latest genetic research to improve the protection and understanding of these threatened fish.
    Science topics Chinook Salmon, Fish, Monitoring methods and techniques, Salmon migration
    Updated April 15, 2026