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  • 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

    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

    Assessing sea-level rise and flooding changes in the Sacramento/San Joaquin Delta using historical water-level records

    Lead California State University [CSU]
    Description The project aims to recover, digitize, and analyze more than 1300 station years of ‘lost-and-forgotten’ water level records collected from 1857 to 1982 in the Sacramento-San Joaquin Delta. These measurements, augmented by modern data, will improve our understanding of tidal, flood, and sea level trends in the system. By determining ‘hotspots’ of habitat and flood risk sensitivity, the results may be used to better focus future scientific and management priorities, to protect the environment, manage flood risk, and enhance community resilience to climate change
    Science topics Backwater, Climate change, Environmental drivers, Estuaries, Land elevation, Levees, Outflow, Sea level rise, Stage, Subsidence, Surface water flow, Tides, Velocity, Vessels and shipping channels, Water, Wind
    Updated October 10, 2023
  • 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

    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 and exports, Water temperature
    Updated May 22, 2025
  • Title

    San Francisco Bay-Delta Estuary 2025 Lidar Mapping Collaboration

    Lead San Francisco Estuary Institute [SFEI]
    Description

    This lidar project provides high-resolution, region-wide elevation data for the San Francisco Bay-Delta Estuary, offering an unprecedented view of the landscape, landforms, and habitat conditions. LiDAR, which stands for Light Detection and Ranging, uses laser pulses to measure the distance between the sensor and the ground, creating detailed three-dimensional maps of terrain. This dataset captures fine-scale features across the San Francisco Bay-Delta Estuary. This supports researchers, community members, and agencies to better visualize changes in topography, habitat distribution, and flood risk. By providing consistent, accurate, and comprehensive coverage, the lidar data supports a wide range of applications. Researchers can use the data to study habitat dynamics, track landscape change over time, model ecological processes, and more. Agencies and planners can integrate the information into flood risk management, infrastructure planning, and climate adaptation strategies. Community organizations and local stakeholders can also use the data to understand environmental conditions in their neighborhoods and inform local projects. The lidar data will be made publicly available following final review in 2026. 

    Availability details and links will be shared here as soon as the data are released. 

    This lidar collection collaboration would not be possible without funding support from the Wetlands Regional Monitoring Program (through funding awarded by the San Francisco Bay Restoration Authority), Delta Stewardship Council, California Department of Water Resources, South Bay Salt Pond Restoration Project, and Valley Water (Santa Clara County). 

    Project Details:

    Area

    ~1.25 million acres (the size of Delaware)

    Timing

    Coordinated with low tides

    Aircraft

    Cessna Caravan

    Sensor

    Riegl VQ-1560ii-S

    Accuracy

    Precise to ~12 cm (height of a soda can!)

    Quality

    Q1 (last LiDAR collection in 2017 was at Q2)
    Science topics None specified
    Updated April 16, 2026
  • Title

    Mossdale Spring Trawl

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    Description

    The Mossdale Trawl occurs two miles downstream of Mossdale Landing County Park (river miles 56), and upstream of the Old River confluence. Timing and production (indices and estimates) for the out-migrating fall-run Chinook salmon smolts has been monitored at this location since 1987. Additionally this trawl captures coded wire tagged Chinook smolts and is the primary capture site for these fish being used to estimate survival of Chinook smolts in the river system. Results from this project, therefore document information on the out-migration timing, survival, and the magnitude of nonmarked smolt production from the San Joaquin Basin passing into the South Delta. The trawl also captures steelhead outmigrants and provides an index of these outmigrants for the entire San Joaquin River Basin.

    Project Need

    This project needs to identify annual juvenile Chinook salmon production in the San Joaquin River Basin. This project provides data supporting water management in the San Joaquin River basin and the Delta. Enumerating steelhead (Oncorhynchus mykiss) migrating through the San Joaquin River into the south Delta. Developing method to differentiate fall and spring run juvenile Chinook salmon migrating in the San Joaquin River basin.

    Project Objectives

    • What is the annual juvenile Chinook salmon production in the San Joaquin River Basin?
    • How do water quantity and quality conditions affect smolt production trends?
    • How many Oncorhynchus mykiss passage at Mossdale trawl?
    Science topics Steelhead Trout
    Updated March 25, 2026
  • Title

    Fish Facilities Monitoring

    Lead California Department of Fish and Wildlife [CDFW]
    Description

    Description

    The Fish Facilities Monitoring program provides database management and quality assurance to the State and Federal fish facilities, which protect and divert fish away from the water project pumping plants. The State Water Project (SWP), operated by the California Department of Water Resources (DWR), and the Central Valley Project (CVP), operated by the U.S. Bureau of Reclamation, export water out of the San Francisco Bay Delta for urban and agricultural use in California. When water is exported, fish become entrained into the diversions. Since 1957, the U.S. Bureau of Reclamation (USBR) has salvaged fish at the Tracy Fish Collection Facility (TFCF). CDFW's Fish Facilities Unit, in cooperation with DWR, began salvaging fish at the Skinner Delta Fish Protective Facility (SDFPF) in 1968. The salvaged fish are released at several sites in the western Delta. Salvage of fish at both facilities is conducted 24 hours a day, seven days a week at regular intervals. Sampling of entrained fish at the SDFPF and TFCF is the source for CDFW's daily salvage and loss estimates for the monitoring of incidental take of listed fish species.

    Project Need

    Fulfills mandates in the 2024 Biological Opinion and the 2024 Incidental Take Permits for Long Term Operation of the State Water Project.

    Project Objectives

    • Provides technical advice and expertise on evaluating fish salvage.
    • Updates the Skinner Fish Facility Operations Manual annually.
    • Determines entrainment of fish toward the water projects.
    • Monitors and reports on the number of fish and of which species are salvaged at the fish facilities.
    • Reports and distributes listed species salvage for Chinook Salmon, steelhead, Longfin Smelt, Delta Smelt, and Green Sturgeon.
    • Manages daily data for distribution.
    • Implements special studies on entrainment, salvage, and loss.
    • Calculates Chinook and Steelhead Salmon loss from the facilities using salvage data.
    • Ensures that fish facility staff are trained in fish identification by providing training and training materials.
    Science topics Fish
    Updated April 8, 2026