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  • Title

    Estimating Abundance of Juvenile Winter-run Chinook Salmon Entering and Exiting the Delta [SAIL]

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

    This is a continuation of a five-year project funded by CDWR and CDFW and the Central Valley Project Improvement Act in 2017. The objective of the project is to improve estimates of population abundances for fall, winter and spring run juvenile Chinook Salmon at Sacramento and Chipps Island by improving trawl efficiency estimates using data from releases of coded wire tags (CWT), acoustic tags (AT), and by genetically sampling the trawl catch in 2025 and 2026. The project will (1) develop statistical models for estimating trawl efficiencies using 2016-2025 data for paired AT-CWT releases of winter run and fall-run Chinook Salmon; (2) use 2016-2025 genetic sampling of trawl catch in combination with efficiency estimates to estimate population abundances of fall, spring and winter run at Sacramento and Chipps Island for 2016-2025; (3) implement trawl efficiency studies for multiple salmon runs in 2025-2026 informed by the prior results and in coordination with hatcheries for inclusion of AT fish with existing CWT releases; and (4) combine trawl efficiencies with genetic samples of trawl catch to provide estimates of fall, spring and winter-run salmon abundance (with estimated precision) entering and exiting the Delta in 2016-2025.

    Science topics Chinook Salmon
    Updated May 19, 2025
  • Title

    Enhanced Delta Smelt Monitoring [EDSM]

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

    Description:
    The Enhanced Delta Smelt Monitoring (EDSM) program is a comprehensive, year-round monitoring initiative that employs multiple research crews conducting concurrent trawling operations across designated strata within the San Francisco Estuary. The program specifically targets post-larval Delta Smelt from April through June using 20mm trawling gear, while Kodiak trawling gear is utilized for the remainder of the year.
    Need:
    The ongoing decline of the Delta Smelt population has underscored the critical need for continuous improvement in the data supporting our understanding of the ecological and anthropogenic factors influencing Delta Smelt population dynamics. The EDSM program plays a vital role in providing essential biological data that informs management strategies aimed at mitigating the adverse effects of water operations on this endangered species. By capturing data across nearly all life stages of Delta Smelt, including near-real-time information on juvenile and adult stages, the EDSM program offers significant conservation benefits. This data is promptly disseminated to the Smelt Working Group and other resource managers to facilitate informed decision-making during the critical entrainment season.
    Objectives:
    -Estimate the total abundance of Delta Smelt, including standard errors or confidence intervals, on a weekly to bi-weekly basis across various life stages (post-larvae, juveniles, sub-adults, adults) throughout the year.
    -Assess the spatial distribution of Delta Smelt at a management-relevant temporal and spatial resolution.
    -Provide data that supports management decisions and addresses scientific inquiries related to sampling efficiency, drivers of Delta Smelt population patterns, and other conservation and management-related topics.

    Science topics Conductivity, Crustaceans, Delta Smelt, Dissolved oxygen, Endangered species, Fish, Invertebrates, Jellyfish, Main channels, Monitoring methods and techniques, Mysis, Other species, Pelagic fish, Salinity, Temperature, Turbidity, Water conveyance / infrastructure, Water management, Water operations / exports, Water temperature
    Updated May 23, 2025
  • Title

    Environmental Monitoring Program: Continuous Water Quality Monitoring

    Lead California Department of Water Resource [DWR]
    Description DWR has conducted water quality monitoring for the California State Water Project since 1968. This program is currently managed by the Division of Operations and Maintenance, Environmental Assessment Branch. Initially, this program sought to monitor eutrophication (an increase in chemical nutrients) and salinity in the SWP. Over time, the water quality program expanded to include parameters of concern for drinking water, recreation, and wildlife. DWR's Division of Operations and Maintenance (O&M) currently maintains 16 continuous water quality monitoring stations located throughout the State Water Project. Data from these automated stations are uploaded to the California Data Exchange Center (CDEC) website. Hourly to daily conductivity, temperature, turbidity, pH, fluorometry, UVA-254 absorption
    Science topics Air temperature, Algae, Chemistry, Chlorophyll A B, Conductivity, Cyanobacteria, Dissolved oxygen, Drought, Environmental drivers, Estuaries, Harmful algal blooms HAB, Nitrogen, Nutrients, pH, Phytoplankton, Primary production, Salinity, Surface water flow, Temperature, Tides, Turbidity, Water, Water conveyance / infrastructure, Water management, Water temperature
    Updated May 21, 2024
  • 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 / infrastructure, Water management, Water operations / exports, Water temperature
    Updated May 21, 2025
  • Title

    Functional diversity and predator dynamics along the Sacramento and San Joaquin River Delta

    Lead University of California - Santa Cruz [UCSC]
    Description This project's objectives are to: 1) determine snake species diversity and relative abundance, 2) establish resources available and examine the functional role that snakes play along field sites within the Sacramento-San Joaquin River Delta, 3) document predator-prey interactions, and 4) assess the thermal physiology of snakes and the thermal profile of microhabitats along the Sacramento-San Joaquin Delta.
    Science topics Habitat, Invasive and non native species
    Updated February 27, 2025
  • Title

    Fish out of breath: Assessing, developing, and validating physiological bioindicators of hypoxia across the Delta

    Lead University of California - San Diego [UCSD]
    Description This proposal seeks to generate two management tools to optimize ongoing conservation efforts (e.g. wetland restoration, fish supplementation) by accomplishing the following 4 objectives: Objective 1) use controlled laboratory experiments to identify temperature-dependent hypoxia tolerance data (Pcrit) for ChinookSalmon smolts and juvenile Delta Smelt. Objective 2) compile existing temperature and DO monitoring data across the SFE. Objective 3) generate metabolic indices using the newly-generated physiological data (Obj. 1) and existing environmentalinformation (Obj. 2) to examine spatial and temporal patterns in metabolic stress for each species. Objective 4) explore and develop an otolith-based bioindicator to identify past hypoxia exposure.
    Science topics Chinook Salmon, Delta Smelt, Dissolved oxygen, Temperature
    Updated February 28, 2025
  • Title

    Harmonizing pesticide risk management of the Bay Delta watershed

    Lead University of California - Santa Barbara [UCSB]
    Description Objective One: Employ high-resolution irrigation data to predict pesticide risks in the Bay Delta Watershed (BDW). This effort will enable more accurate prediction of health hazards given irrigation is a key driver of pesticide transport to surface and ground water. The effects of irrigation methods to pesticide transport vary significantly in their contribution of pesticides to runoff/leachate due to effects on pesticide build-up/wash-off and soil moisture conditions antecedent to precipitation. Objective Two: Provide harmonized species indicators of pesticide toxic burden releases for the Bay Delta which consider diverse resident taxa and human health. California benefits from a plethora of academic researchers, environmental advocacy groups, municipalities, and government groups working to protect the environment. Due to the complexities of this work, efforts often focus on a particular taxa or environmental compartment. This introduces a significant challenge in evaluating the pros and cons of any particular pesticide use. Currently, 79 of the 208 watersheds near the Delta which receive agricultural pesticide applications have increasing pesticide toxic burdens to aquatic taxa. Enabling evaluation of chemical alternatives which reduce toxic burdens across taxa is important to restoring ecosystem health. Objective Three. Quantify the variability of pesticide degradation and the significance to pesticide risk in the BDW. The degree to which pesticides remain in the soils of the BDW increases their probability for accumulation, transport, and nontarget affects. Degradation is highly variable in soils; an investigation of 10 pesticides in 8 soil types under equivalent conditions demonstrated a mean difference of 540% in the minimum and maximum rate of degradation for pesticides evaluated. Yet, researchers and regulators often only employ the median observed rate of degradation which may under predict risks to waterbodies of the BDW.
    Science topics Pesticides
    Updated February 27, 2025
  • Title

    Examining the relationship between Longfin Smelt and flow in the San Francisco Bay Delta

    Lead University of California - Berkeley [UC Berkeley]
    Description The number of longfin smelt in the San Francisco Estuary has been in decline for the past several decades. While decreased freshwater flow reaching the estuary has been identified as a contributing factor, the relationship between flow and smelt populations has proven complex and appears to be changing over time. This study examined how water flow affects longfin smelt populations across different habitats in the San Francisco Estuary, analyzing decades of monitoring data from state and federal agencies. The research explored both where smelt live in the estuary and how their populations change over time in response to varying water flows. The findings show that more freshwater flow generally helps smelt populations, especially young fish in shallow waters. However, this beneficial effect appears to be weakening over time in some areas, particularly in open waters away from the shore. This suggests that smelt may be adapting to changing conditions by moving to different parts of the estuary. To help protect this threatened species, conservation efforts may need to focus on both restoring natural water flows and improving habitat conditions throughout the estuary.
    Science topics Fish, Flows, Longfin Smelt, Zooplankton
    Updated February 27, 2025
  • 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

    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

    Continuous Flow and Water Quality Monitoring Network in the Sacramento-San Joaquin Delta

    Lead U.S. Geological Survey [USGS]
    Description This project envisions the continuation, expansion, and further integration of high frequency monitoring for flow, water quality (including chlorophyll and nutrients), sediment, as well as biological responses at key locations in the Delta and Suisun Bay. The physical properties monitored by the fixed-station network are the primary drivers of the habitat conditions and biological responses that management actions hope to achieve. Nutrient dynamics are explicitly measured at select stations to improve our understanding of how physical dynamics, water quality and landscape features shape the base of Delta food webs. These data will provide information about drivers linked to food quantity and quality as well as potential toxins production by harmful algae. Suspended-sediment monitoring provides an understanding of the inputs and internal exchanges between regions, locations of sources and sinks, and provides insight into the underlying cause of turbidity variability in the study area. Suspended-sediment measurements gage the availability of suspended sediment for existing marshes and for proposed large-scale marsh restoration efforts in the Delta. There are a total of 4 teams associated with this work: • Hydrodynamics Team – Fixed Station Network Operation and Maintenance (Flow, Velocity, Gage Height, Core WQ) • BioGeoChemistry Team -- Fixed Station Network Operation and Maintenance (Expanded WQ, Nutrients, Phytoplankton) • Delta Sediment Team – Fixed Station Network Operation and Maintenance (Suspended Sediment, Delta) • Bay Team – Fixed Station Network Operation and Maintenance (Suspended Sediment and WQ in SF Bay)
    Science topics Chlorophyll A B, Conductivity, Dissolved oxygen, Flows, Nutrients, pH, Phytoplankton, Sediments, Stage, Surface water flow, Tides, Turbidity, Velocity, Water operations / exports, Water temperature
    Updated May 22, 2025
  • Title

    Analysis of Delta Salinity during Extended Drought – Pilot Project

    Lead California Department of Water Resource [DWR]
    Description Managing California water operations for multiple priorities under long term drought conditions is becoming an increasing challenge which is compounded by potential sea level rise. This project is a pilot exercise to demonstrate the utility of hydrodynamic and salinity transport models in to understand options for salinity management under extended drought combined with climate change and sea level rise. The project will also consider how to make model outputs available and relevant to other modeling and environmental management decision making efforts. The full range of potential sea level rise, restoration and operational actions is extensive, involving many potential combinations of individual actions. Therefore, it is difficult to fully explore potential actions with high resolution multi-dimensional models. The proposed approach is to use high resolution multi-dimensional flow and transport models to evaluate changes in transport in the Delta under sea level rise, restoration, and operational scenarios. The predicted changes to salinity for a given scenario will inform operations modeling in CALSIM through re-calibration of an ANN to approximately account for the changed salinity response of the estuary. Operations modeling incorporating the revised ANN will then estimate Delta inflows and overall water cost to meet Delta standards for the scenario. “Round-trip” modeling will be performed using the detailed Delta models to verify that the predicted hydrologic inputs allow appropriate compliance with water quality standards and will provide other metrics related to Delta transport.
    Science topics Conductivity, Drought, Landscape change, Restoration planning, Sea level rise, Water operations / exports
    Updated June 14, 2024
  • Title

    Developing novel non-invasive environmental RNA (eRNA) tools for conservation of two endangered Bay-Delta fish species

    Lead University of California - Davis [UC Davis]
    Description

    Due to pervasive anthropogenic influences (e.g., habitat alteration, climate change), current rates of biodiversity loss in the Sacramento-San Joaquin Delta are unprecedented. Application of appropriate management regimes and mitigation measures thus require effective biological monitoring to adaptively manage systems. Non-invasive environmental DNA (eDNA)-based tools for endangered species monitoring have gained attention as a complementary approach to traditional sampling because of their increased sensitivity and accurate quantification. However, the unique characteristics of environmental RNA (eRNA) make it a novel tool, allowing us to gain additional information that is not possible to obtain with eDNA. Using novel eRNA tools to improve detection and quantify health status of Smelt has only been theorized and remains to be empirically tested. Both Delta and Longfin Smelt species were historically ubiquitous in the Sacramento-San Joaquin Delta, but have declined precipitously over the past several decades. One source of mortality is entrainment into the south Delta water export pumps. Although the entrainment of juvenile and adult smelt has been regularly monitored at fish salvage facilities, entrainment of larval smelt (< 20 mm) is not quantified, thus remains largely unknown. Moreover, given the current climate change effect (e.g., increased heat stress), an understanding of how these endangered species will respond to acute stress response in the wild is lacking.

    Science topics Delta Smelt, Longfin Smelt
    Updated April 10, 2025