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  • Title

    Delta Aquatic Resource Inventory

    Lead Sacramento-San Joaquin Delta Conservancy
    Description The Delta Aquatic Resources Inventory of surface waters, wetlands and other aquatic resources in the Sacramento-San Joaquin Delta (Delta) will provide a standard regional approach to wetland classification and mapping to support wetland restoration planning, tracking, and reporting. It will faciliate implementation of the California Wetland and Riparian Areas Monitoring Plan (WRAMP) in the Delta.
    Science topics Wetland mapping
    Updated November 17, 2022
  • Title

    Quantifying Biogeochemical Processes through Transport Modeling: Pilot Application in the Cache Slough Complex

    Lead University of California - Davis [UC Davis]
    Description Funding for this project will focus on observations and hydrodynamic models of the Cache Slough Complex. To accomplish this, the project implementation will involve making extensive use of models developed in ongoing CDFW-funded projects. These projects have included the development and initial calibration of a two-dimensional hydrodynamic model of the Cache Slough Complex. The model utilizes the Deltares Flexible Mesh numerical model, an open-source hydrodynamic model applied in a growing number of studies in the Bay/Delta system. Work is continuing in that project to refine the model calibration within the Cache Slough Complex and extend the calibrated period. The model is also being applied to study how tidal forcing and channel configuration shape the hydrodynamic connections between parts of the system.
    Science topics None specified
    Updated November 18, 2022
  • Title

    Low-Cost Satellite Remote Sensing of the Sacramento-San Joaquin Delta to Enhance Mapping for Invasive and Native Aquatic Vegetation

    Lead University of California - Davis [UC Davis]
    Description Invasive aquatic vegetation (IAV) acts as an ecosystem engineer by changing habitat conditions and water quality. This negatively affects the survival of native species. Over the past 15 years, IAV has more than doubled its footprint in the Sacramento-San Joaquin Delta waterways. The State of California spends millions of dollars each year to control IAV in the Delta-Suisun region and costs are likely to continue to rise. Gaining a better understanding of the spread, life history characteristics, and potential vulnerabilities of these species can lead to more effective control strategies. The recent launch of the Sentinel-2 satellite can fill temporal gaps left by annual airborne surveys. This study will create a data pipeline for sustained, low-cost satellite-based monitoring of aquatic and marsh vegetation year-round. To quantify one of the Delta Plan performance measures, the time and degree of floodplain inundation for the Yolo Bypass will be measured. This study will result in new metrics to measure progress toward habitat goals in several restoration sites.
    Science topics Aquatic vegetation, Invasive / non native species
    Updated October 3, 2024
  • Title

    Tidal Wetland Restoration in the Bay-Delta Region: Developing Tools to Measure Carbon Sequestration, Subsidence Reversal, and Climate Resiliance 2021

    Lead California State University [CSU]
    Description Tidal marshes are important ecosystems in the San Francisco-Bay Delta. They remove carbon from the atmosphere, build up soils that buffer our communities from sea level rise, mitigate excessive nutrients (like nitrogen), and provide critical habitat and food resources for a diversity of species. It is difficult to predict how tidal marshes change naturally over time versus as a response to climate change, restoration and water quality changes. This project provides the first ever multi-year dataset of the complete carbon budget of a tidal marsh. This dataset will be used to predict seasonal and annual carbon budgets in tidal marshes over a range of salinities. The model will assess the sustainability of existing and potential restored tidal wetland benefits over the next 100 years using remote sensing data. The model will be an open-source tool designed for use by wetland managers and decision makers in the Bay-Delta region. This project supports ongoing initiatives to restore tidal wetlands in the Delta and our ability to manage them in a changing world.
    Science topics None specified
    Updated April 29, 2022
  • Title

    An Improved Genomics Tool for Characterizing Life History Diversity and Promoting Resilience in Central Valley Chinook Salmon

    Lead Michigan State University
    Description This study will improve our ability to protect the diversity of traits in Chinook salmon. The diversity of Chinook salmon migration timing is decreasing in the Central Valley. A key roadblock to protecting diversity is the current inability to rapidly and inexpensively identify large numbers of individuals from different populations during their migration to the ocean. This study addresses this information gap by leveraging pre-existing genomic data to develop a new technique that will allow scientists to identify individuals to life history type and location. For example, this study will potentially be able to identify Fall Run Chinook that are from the Sacramento versus the San Joaquin River basins. This information, in combination with data on water temperature and river flows, can determine the relationship between environmental conditions and juvenile salmon life history diversity. The information generated by this work will provide managers with the ability to accurately monitor the effect of key management actions on the different Central Valley Chinook salmon populations.
    Science topics Chinook Salmon, Estuaries, Fish, Habitat restoration, Resilience, Salmon rearing
    Updated November 29, 2022
  • Title

    Pesticide risk analyses and management actions, chemical fate and transport

    Lead University of California - Santa Barbara [UCSB]
    Description

    This project work will model the risk of pesticide pollution in 225 sub-catchments of the Sacramento-San Joaquin Bay-Delta. The model will account for water management practices, land use, pesticide use rates, and cumulative pesticide stress. Additionally, this work will produce a web-based tool to simulate current and future risks based on the ranking of primary sources of pesticide contribution. This work will provide a framework to predict risk from chemical stressors. Specific objectives are: (1) enhanced pro-active chemical risk assessment, (2) creation of a tool which enables science-based chemical use decisions, (3) improved risk screening for vulnerable areas, and (4) identification of adverse effects of current and future chemical use strategies.
    Science topics Herbicides
    Updated February 27, 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 / transition zones, Invasive / non native species, Invertebrates, Jellyfish, Main channels, Monitoring methods and techniques, Mysis, Open water, Other species, Pelagic fish, Salinity, Salmon migration, Salmon rearing, SAV/FAV, Steelhead Trout, Turbidity, Water conveyance / infrastructure, Water management, Water operations / exports, Water temperature
    Updated May 21, 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

    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 / 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

    From Microbes to Zooplankton, What Defines a Beneficial Wetland?

    Lead San Francisco State University, Estuary & Ocean Science Center
    Description Our study will characterize species diversity at multiple levels of biological organization in the water column of restoring wetlands in the upper San Francisco Estuary and Delta (SFE), from bacteria to fishes. In doing so, we will also describe the foodweb benefits being provided to larval fishes, including longfin smelt, through additional dietary DNA analysis. We will use the species diversity we find in the water column to identify a subset of biota that are indicative of the conditions present in wetlands in different stages of restoration (early, intermediate, and mature) and identify connections between those indicators to the foodweb resources being provided to higher trophic levels. We will study 3-4 wetlands in each of 3 stages: early (unvegetated), intermediate (partially vegetated and partially channelized), and mature (fully vegetated and channelized) wetlands.
    Science topics Crustaceans, Cyanobacteria, Estuaries, Fish, Food webs, Habitat, Habitat restoration, Insects, Invertebrates, Longfin Smelt, Other species, Other zooplankton, Pelagic fish, Phytoplankton, Predation, Restoration, Salinity, Saltwater / freshwater marshes, Tidal wetlands, Wetlands, Zooplankton
    Updated January 31, 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 / transition zones, Invasive / 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

    Pixel-Wise Footprint Analysis of GPP Using High-Resolution NDVI/NIRv Data

    Lead University of California - Berkeley [UC Berkeley]
    Description Spectral indices such as NDVI have long been found to be good predictors of plant productivity at many spatial scales from the canopy to the landscape. Spectral indices are an important tool for upscaling GPP fluxes we measure at the ecosystem scale through Eddy Covariance up to larger spatial scales. Other indices, such as NIRv (expressed as NDVI * total NIR) have also been shown to be potentially more accurate predictors of GPP using in-situ spectral measurements than NDVI alone. Additionally, associating spectral signals within modeled flux footprint areas has been shown to improve the predictive capability of spectral indices compared to estimates using remotely sensed data centered directly on top of flux towers. Most if not all of these spatially explicit footprint analyses have been done by aggregating footprints into polygons based on their 50%-90% estimated flux contributions, and then associating those polygons with fluxes and spectral signals within them. This approach has been necessary largely because of the spatial scales involved with satellite remote sensing products, reaching a practical minimum of 3m, downsampled from 4.8m imagery by Planet Labs. By combining pixel-weighted flux footprint contributions with ultra-high resolution (3cm) spectral drone data, we will examine and compare how different spatial scales and indices affect the capability of spectral data to predict fluxes which are not directly measured.
    Science topics None specified
    Updated January 30, 2024
  • Title

    Plant traits of Vallisneria australis

    Lead California State University [CSU]
    Description Individual clones/plants of Vallisneria australis were sampled from a Delta location. Specimens were sampled from the center of each patch (<200 m2) or bed (≥200 m2) to control for variation within each bed. Four (4) individual plants (rhizome with complete vertical shoots) were collected by hand and transported back to the laboratory in Ziplocs. Leaves per shoot, leaf area, shoot height, shoot width, rhizome length, rhizome diameter along the internodal segment of the main rhizome, and wet and dry biomass were measured for all plants. Those data are included in this Science Tracker report.
    Science topics Invasive / non native species
    Updated August 18, 2024