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Title	Identifying the Causes of Feminization of Chinook Salmon in the Sacramento and San Joaquin River System
Lead	University of California - Berkeley [UC Berkeley]
Description	Purpose was to assess the potential importance of endocrine-disrupting chemical contaminants to salmon and other resident speices of waters that are discharged into the San Francisco-San Joaquin Delta.
Science topics	Chinook Salmon
Updated	April 29, 2022

Title	How Abiotic Processes, Biotic Processes, and Their Interactions Sustain Habiata Charactersitics and Functions in River Channels and Their Floodplains: An Investigation of How a Reach of the Merced River Responds to Restoration
Lead	University of California - Santa Barbara [UCSB]
Description	The purpose of this project is to determine how river restoration affects the abundance and distribution of salmonid and non-salmonid fishes at critical life stages. The proposal involves field survey of hydraulics, sedimentation processes, channel changes, habitat conditions, invertebrate and fish communities and their interactions.
Science topics	None specified
Updated	April 29, 2022

Title	Review of Four Juvenile Salmon Coded Wire Tag Experiements Conducted in the Delta
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The US Fish and Wildlife Service, Stockton Fish and Wildlife Office, has since the mid-1980s conducted several multi-year release-recovery experiments with coded-wire-tagged juvenile Chinook salmon. The objectives of the studies were (1) to estimate survival through the lower portions of the Sacramento and San Joaquin river systems, the California Delta, and (2) to quantify the factors affecting survival. Four of these studies, listed more or less by their historical start dates, are the Delta Cross Channel, Interior, Delta Action 8, and VAMP experiments.
Science topics	Chinook Salmon
Updated	April 29, 2022

Title	Predicting the Effects of Invasive Hydrozoa [Jellyfish] on Pelagic Organisms Under Changing Salinity and Temperature Regimes
Lead	University of California - Davis [UC Davis]
Description	The purpose of this project seeks to investigate the potential effects of jellyfish, a devising invader of some ecosystems, on the SFE ecosystem, to determine the key factors allowing successful establishment and spread of these species, and to predict future effects and spread of the invasions.
Science topics	Water temperature, Salinity, Pelagic fish, Jellyfish
Updated	April 29, 2022

Title	Climate change impacts to San Francisco Bay-Delta wetlands: Links to pelagic food webs and predictive responses based on landscape modeling
Lead	San Francisco State University [SFSU]
Description	The purpose of this project is to 1) evaluate the potential impacts of climate change on SF Bay-Delta tidal wetlands, 2) improve our understanding of the linkage between these wetlands and the pelagic food web, especially fish populations, and 3) use this information to make predictions about potential effects of climate change on Bay-Delta fish populations.
Science topics	Pelagic fish, Wetlands
Updated	April 29, 2022

Title	Quantitative Indicators and Life History Implications of Environmental Stress on Sturgeon
Lead	University of California - Davis [UC Davis]
Description	The purpose of this project is to analyze the effects of the pollutants on the overall fitness of different life stages of the green and white sturgeon. This research will significantly enhance our understanding of stressors on sturgeon and allow further development of life history models.
Science topics	Water temperature, Salinity, Pelagic fish, Methylmercury, Sturgeon
Updated	April 29, 2022

Title	Comparison of Nutrient Sources and Phytoplankton Growth and Species Composition in Two Rivers: Their Roles in Determining Productivity and Food Web Conditions in Suisun Bay and the Delta
Lead	San Francisco State University [SFSU]
Description
Science topics	Phytoplankton, Pelagic fish, Nitrogen and ammonia
Updated	April 29, 2022

Title	The Transport and Dispersion of Rafting Vegetation in the Sacramento-San Joaquin Delta
Lead	University of California - Berkeley [UC Berkeley]
Description	The research we are proposing here is focused on developing a thorough, mechanistic understanding of how rafting vegetation, such as hyacinths or egeria, is transported in the Sacramento-San Joaquin Delta. Our approach is to examine in detail the forces that act on rafts of vegetation, and the resulting raft accelerations, to establish a predictive model of raft pathlines. Our model development will be built around a series of field experiments that include measurements of raft movement using GPS-logging drifters integrated into rafts, tidal and wind-forcing using a boat mounted current profiler and an anemometer, and direct estimation of the water-induced shear stress using a point velocity meter incorporated into the actual rafts. These field observations will be used to critically evaluate a numerical model of both channel (tidal) flows and resulting raft movement. Our initial development will include a highly-resolved channel flow model, which will explicitly capture more lateral variability, including low velocity side "pockets", than is typically resolved with Delta scale hydrodynamic models. Initially, this will allow us to carefully evaluate the quality of our raft tracking calculations. Once the approach is established to be accurate, however, these high-resolution flows will be used to numerically calculate the effective advection and dispersion of rafts in the Delta channel under consideration. This analysis will be focused on parameterizing the effects on raft transport of structures and processes that are unresolved in typical Delta hydrodynamics models. An example of a process that is likely to be important to parameterize is the trapping and retention of rafts along the perimeter of channels due to off-axis wind forcing, and the resulting along-channel dispersion of rafts. In order to examine the effective advection and dispersion of rafts in Delta channels, we propose to pursue this combination of field and numerical studies of raft transport in locations of increasing complexity: first in idealized, straight channels, then in a natural, sinuous channel and a channel junction, and finally throughout the entire Delta. Our research is strongly motivated by the desire to provide a predictive model of dispersion in the Delta for floating objects that respond to both wind and tidal forcing. Immediate applications involve the movement of hyacinth rafts and egeria to evaluate potential management strategies. Important future applications are likely to include consideration of other biological invasions, due to the potential for rafts to provide a transport pathway, and analysis of the movement of accidental or intentional releases of floating material in the Delta.
Science topics	None specified
Updated	November 12, 2025

Title	The Consequences of Operational Decisions on Water Quality: Reconciling Delta Smelt, Salmon, and Human Needs
Lead	Contra Costa Water District [CCWD]
Description	The purpose of this project is to assess the consequences of actions taken to protect threatened or endangered Chinook salmon species relative to other upstream and in-Delta water management actions that have changed seasonal salinity in the Delta, thus reducing the ability of delta smelt to survive as a species;and, to investigate with modeling scenarios the potential to ameliorate this trade-off with specific operational actions.
Science topics	Delta Smelt, Chinook Salmon
Updated	April 29, 2022

Title	A Calibration-Free Approach to Modeling Delta Flows and Transport
Lead	University of California - Berkeley [UC Berkeley]
Description	The purpose of this project is to develop and evaluate an integrated system for the prediction of Delta flows and transport in real-time that doesn't rely upon historical data sets for calibration and validation. The system consists of observational and computational components, along with real-time communication and coordination.
Science topics	None specified
Updated	April 29, 2022

Title	Pilot Mark-Recapture Study to Estimate Delta Smelt Pre-Screen Loss and Salvage Efficiency
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The purpose of this project is to perform a study to determine whether it is feasible to quantify entrainment losses of juvenile and adult delta smelt due to water exports. This information is critical to better understanding the movement of Delta smelt in the system.
Science topics	Delta Smelt
Updated	April 29, 2022

Title	Are Apparent Sex Reversed Chinook Salmon a Symptom of Genotoxicity?
Lead	University of California - Davis [UC Davis]
Description	Goal was to test the relative importance of chemical stressors on population viability and genetic diversity for fall-run Chinook salmon (in association with environmental contaminant exposure in the Central Valley delta).
Science topics	Chinook Salmon
Updated	April 29, 2022

Title	Using Flowcam Technology to Measure High Frequency Spatial and Temporal Variation in Phytoplankton and Zooplankton Species Composition and Develop State-of-the-Art Plankton Monitoring
Lead	California Department of Water Resource [DWR]
Description	The purpose of this project is to use the new imaging-in-flow instrument FlowCAM to rapidly and automatically identify, enumerate and estimate biomass for in situ and laboratory phytoplankton and zooplankton species composition samples in the SF Estuary.
Science topics	Phytoplankton, Zooplankton
Updated	April 29, 2022

Title	A Non-Point Source of Contaminants to the Estuarine Food Web: Mobilized Particles from the Intertidal Zone
Lead	California State University [CSU]
Description	The purpose of this research project is to quantify the process of contaminant concentration and resuspension of shallow and intertidal cohesive sediments at sites along the salinity gradient from Prospect Island to San Pablo Bay. This research is important because it helps to understand the pathways by which contaminants are assimilated, which is essential to appropriately manage habitat areas.
Science topics	None specified
Updated	April 29, 2022

Title	Estimating Juvenile Chinook Salmon Spring and Winter Run Abundance at Chipps Island
Lead	U.S. Fish and Wildlife Service [USFWS]
Description	The purpose of this project will develop and implement a DNA sampling protocol for juvenile Chinook salmon captured at Chipps Island.
Science topics	Chinook Salmon
Updated	April 14, 2026

Title	Analysis of Archived Samples to Assess Patterns of Historic Invasive Bivalve Biomass
Lead	California Department of Water Resource [DWR]
Description	The purpose of this project is to provide information regarding the effect of bivalves in restored habitat by assessing patterns of invasive bivalve biomass. This research is important because these bivalves are invasive and dominant in the upper SF Bay-Delta system, which are considered to be a major sink of primary productivity in the system.
Science topics	Bivalve
Updated	April 29, 2022

Title	A Statistical Model of Central Valley Chinook Incorporating Uncertainty
Lead	R2 Resource Consultants Inc.
Description	The purpose of this project is to develop a statistical modeling approach to the two Central Valley Chinook Salmon species that incorporates mortality in all phases of salmon life history, and includes the effects of uncertainty in assessing population status, guiding future research, and making management decisions.
Science topics	Chinook Salmon
Updated	April 29, 2022

Title	Foodweb Support for the Threatened Delta Smelt and Other Estuarine Fishes in Suisun Bay and the Western Sacramento-San Joaquin Delta
Lead	San Francisco State University [SFSU]
Description	The purpose of the project is to increase understanding of the foodweb supporting delta smelt and other estuarine species. This research is important because: 1) it could lead to increased foodweb support for the threatened delta smelt and 2) identify potential mechanisms underlying relationships of abundance or survival of some fish to freshwater flow.
Science topics	Delta Smelt
Updated	April 29, 2022

Title	Life History Variation in Steelhead Trout and the Implications for Water Management
Lead	University of California - Santa Cruz [UCSC]
Description	The purpose of this project is to explore the ways in which different stream hydrology and temperature can affect the growth and maturation of steelhead trout. Model examination will incude various stream flow management regimes may affect trout population dynamics region-wide.
Science topics	Steelhead Trout
Updated	April 29, 2022

Title	CASCaDE: Computational Asessments of Scenarios of Change for the Delta Ecosystem
Lead	U.S. Geological Survey [USGS]
Description	Agencies of the CALFED Bay-Delta Authority (CBDA) face tough decisions as they search for strategies to meet their programmatic goals of stabilizing water supplies in California, providing safe drinking water to a growing population, and sustaining diverse populations of native species and their supporting ecosystem functions. The challenge of finding balanced solutions to these goals is daunting because of the enormous complexity of the San Francisco Bay-Delta system and its tributary rivers and their watersheds. The challenge grows as we consider the additional layer of complexity imposed by the certainty that all the key forces that drive dynamics of this ecosystem (climate, hydrology, water management, land use, sea level) will change significantly in future decades. This proposal describes a model-based approach for developing a long view of the Bay-Delta-River-Watershed system. The long view will be developed through simulations with linked models to project changes under a range of plausible scenarios of global warming, hydrologic responses, land-use change, reconfigurations of within-Delta habitats, and sea level rise. Our goals are to develop and apply a model-based approach of ecological forecasting to project future states of the Delta ecosystem under prescribed scenarios of change, and to communicate the outcomes of those scenarios to resource managers facing the daunting challenge of meeting CBDP goals in a continually changing world.
Science topics	None specified
Updated	November 18, 2022

Title	Survivial and Migratory Pattern of Central Valley Juvenile Salmonids
Lead	University of California - Davis [UC Davis]
Description	The purpose of this project is to determine the survival and movement patterns of late-fall Chinook salmon smolts and steelhead smolts as they migrate downstream. This information is important to better understand how salmon move through the system.
Science topics	None specified
Updated	April 29, 2022

Title	Phytoplankton Communities in the San Francisco Estuary: Monitoring and Management using a Submersible Spectrofluorometer
Lead	California Department of Water Resource [DWR]
Description	The purpose of this project is to evaluate a new submersible spectrofluorometer, the bbe FluoroProbe, for phytoplankton monitoring and management in the SFE. Secondly, this project seeks to investigate high-frequency patterns in spatial phytoplankton group distributions among Delta habitats and along gradients from the western Delta and northern San Francisco Bay.
Science topics	None specified
Updated	April 29, 2022

Title	Modeling the Delta Smelt Population of the San Francisco Estuary
Lead	San Francisco State University [SFSU]
Description	The purpose of this project is to develop an individual-based particle-tracking model examining population behavior of Delta smelt under different scenarios.
Science topics	Delta Smelt
Updated	April 29, 2022

Title	Biomass and Toxicity of a Newly Established Bloom of the Cyanobacteria Microcystis aeruginosa and its Potential Impact on Beneficial Use in the Sacramento-San Joaquin Delta
Lead	California Department of Water Resource [DWR]
Description	Monitoring and simple analysis of the extent of this cyanobacteria in the Delta, and preliminary exploration of the impacts of cystins on drinking water quality, and human and wildlife health.
Science topics	None specified
Updated	April 29, 2022

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