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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	Yolo Bypass Salmonid Habitat Restoration and Fish Passage: Scenario Analysis of Fremont Weir Notch – Integration of Engineering Designs, Telemetry, and Flow Fields
Lead	U.S. Army Corps of Engineers [USACE]
Description	This study analyzes 12 notch scenarios in the Fremont Weir in terms of entrainment of juvenile salmon. The goal is to quantify the relative entrainment rates (between 0 and 1) across the suite of scenarios and to identify possible strategies for enhancing entrainment outcomes. This study does not predict future entrainment as models generally do not predict future outcomes so much as highlight trends
Science topics	Chinook Salmon, Endangered species, Water conveyance / infrastructure
Updated	April 29, 2022

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 / transition zones, Invasive / non native species, Invertebrates, Longfin Smelt, Main channels, Nitrogen, Nitrogen / ammonia, Nutrients, Other species, Other zooplankton, Pelagic fish, pH, Phytoplankton, Primary production, Sacramento Splittail, Salmon migration, Salmon rearing, Saltwater / freshwater marshes, SAV/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	Science for adaptive management of juvenile spring-run Chinook salmon in the San Joaquin River
Lead	University of California - Davis [UC Davis]
Description	Spring-run Chinook salmon rehabilitation efforts are intensifying on the San Joaquin River. Over the last three years, UC Davis has successfully tracked movement, behavior, reach-specific survival, and route selection for reintroduced juvenile spring-run Chinook salmon in this ecosystem. In 2019, information on salmon tracking was combined with state-of-art habitat (fast limnological automated measurements or “FLAMe”) and physiological (e.g. fish condition, survival and transcriptomic) approaches. Results from this work are ongoing but have yielded actionable information on key habitats and management strategies for promoting salmon life-cycles in the San Joaquin River and central Delta. Now UC Davis will further explore promising recent findings. First, the analysis of an additional year of juvenile salmon tracking will occur to glean more survival information across different water year conditions. This information would be married with expanded FLAMe surveys in space and time along with a second year of physiological assays using caged fish. UC Davis will also evaluate the ‘transport effect’ on salmon, in an attempt to explain consistently high losses of JSATS-tagged salmon through the restoration area. Numerous other synergies exist with new and ongoing telemetry work that will be benefitted by a continuation of this work. The goal is to provide actionable science, and open access data, with a high potential to facilitate adaptive management in the San Joaquin River and central Delta.
Science topics	Chinook Salmon, Endangered species, Estuaries, Fish, Habitat restoration
Updated	October 3, 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	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	December 26, 2023

Title	In search of refuge: Investigating the thermal life history of Delta Smelt through in-situ oxygen isotope ratio analysis of otoliths.
Lead	University of California - Davis [UC Davis]
Description	The inner ear bones of fish, or otoliths, grow continuously and their chemistry reflects the water conditions that a fish has experienced throughout its life. In this project, researchers used in-situ chemical analysis to determine the oxygen isotopic composition of otoliths, which can reflect the water temperature that a fish has experienced. They applied this method to archived adult Delta Smelt otoliths from multiple different water years spanning the time from before and during the recent drought. Using these data, they investigated the relationship between delta smelt abundance and environmental parameters, such as water temperature. More specifically they investigated whether delta smelt are able to find temperature refuges, even in drought years.
Science topics	Climate change, Delta Smelt, Endangered species, Fish, Temperature
Updated	February 26, 2024

Science activities

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Yolo Bypass Salmonid Habitat Restoration and Fish Passage

Yolo Bypass Salmonid Habitat Restoration and Fish Passage: Scenario Analysis of Fremont Weir Notch – Integration of Engineering Designs, Telemetry, and Flow Fields

Yolo Bypass Fish Monitoring

Science for adaptive management of juvenile spring-run Chinook salmon in the San Joaquin River

Non-Invasive Environmental DNA Monitoring to Support Tidal Wetland Restoration

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

In search of refuge: Investigating the thermal life history of Delta Smelt through in-situ oxygen isotope ratio analysis of otoliths.