This study focuses on understanding how restored tidal wetlands with different physical configurations function as refuge and rearing habitat for fishes, including native and imperiled species such as delta smelt and juvenile Chinook salmon. This research will assess the spatial distribution of predation risk as it varies within and across tidal wetlands. The proposed research will generate a statistical model that helps predict predation outcomes from various restored tidal wetland designs and channel configurations. This will be a powerful tool for managers to forecast how proposed habitat restoration or water management actions may impact native fish populations.
The goal of this research is to better understand how climate change will affect fishes with different life histories and habitat associations across the San Francisco Estuary. Existing datasets will be incorporated in synthetic analyses and cutting-edge statistical models to identify fish community responses to climate, flows, and habitats along the estuarine salinity gradient. This synthesis-science project will use rich long-term datasets that have been collected by Bay-Delta researchers for decades that will then be analyzed in a reproducible and open science framework. It will also support efforts by the Interagency Ecological Program’s Climate Change Project Work Team.
This study will investigate fish swim performance in response to temperature, using salmon and two of its known predators: largemouth bass and Sacramento pikeminnow. The researcher will assess swim performance metrics and predation risk inside and outside the ideal thermal range of each species to determine if a temperature advantage predicts salmon survival in predation scenarios. This project’s results will provide a mechanistic understanding of how temperature stress may influence mortality risk of juvenile Chinook salmon through predation, which will offer a more holistic perspective on the management of this species
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.
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.
Description The purpose of this study is to expand IEP monitoring and inference to other dominant near-shore, littoral habitats not sampled by beach seines through the use of boat electrofishing. To accomplish this we will sample key littoral fish species across various near-shore habitats in order to determine how best to estimate abundance, occupancy, capture probabilities, and related environmental drivers. Need Expanding DJFMP sampling to other habitats throughout the Delta will allow our program to detect and monitor fishes and ecological trends through time, alleviating a recognized data gap. Current sampling relies on data collected through non-random fixed point sampling of unobstructed habitats, which limits the utility of our data to inform management decision. Objectives • Design boat electrofishing survey methods to expand DJFMP’s monitoring into habitats and locations not sampled by beach seining. • Design and develop field and data analysis methods for estimating capture probability and abundance using boat electrofishing techniques. • Predict spatio-temporal distribution of habitats occupied by key littoral species.
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.
Tradeoffs among objectives in natural resource management can be exacerbated in altered ecosystems and when there is uncertainty in predicted management outcomes. Multicriteria decision analysis (MCDA) and value of information (VOI) are underutilized decision tools that can assist fisheries managers in handling tradeoffs and evaluating the importance of uncertainty. We demonstrate the use of these tools using a case study in the Sacramento River, California, U.S.A., where two imperiled species with different temperature requirements, winter-run Chinook Salmon (Oncorhynchus tshawytscha) and Green Sturgeon (Acipenser medirostris), spawn and rear in the artificially cold Shasta Dam tailwater. A temperature-control device installed on Shasta Dam maintains cool water for Chinook Salmon; however, uncertainties exist related to the effects of temperatures on the spawning and rearing of both species. We consider four alternative hypotheses in models of early life-stage dynamics to evaluate the effects of alternative temperature-management strategies on Chinook Salmon and Green Sturgeon management objectives. We used VOI to quantify the increase in management performance that can be expected by resolving hypothesis-based uncertainties as a function of the weight assigned to species-specific objectives. We found the decision was hindered by uncertainty; the best performing alternative depends on which hypothesis is true, with warmer or cooler alternative management strategies recommended when weights favor Green Sturgeon or Chinook Salmon objectives, respectively. The value of reducing uncertainty was highest when Green Sturgeon was slightly favored, highlighting the interaction between scientific uncertainty and decision makers’ values. Our demonstration features MCDA and VOI as transparent, deliberative tools that can assist fisheries managers in confronting value conflicts, prioritizing resolution of uncertainty, and optimally managing aquatic ecosystems.
This project aims to test the feasibility of using novel acoustic transmitters to track Delta smelt in the San Francisco Bay-Delta. Successful utilization of acoustic telemetry to track Delta smelt can provide researchers and resource managers with information about the species’ habitat preferences, the effects of water-management practices on Delta smelt movement and distribution, and the success of ongoing supplemental release efforts. The assessment of feasibility will include a comprehensive analysis of both the lethal and sublethal effects of surgical tag implantation on Delta smelt, as well as the development of a species-specific tagging protocol.
Bridging Science and Community: Engaging Youth in Delta Conservation through the Spinning Salmon Program is designed to enhance scientific understanding and engagement among underrepresented youth in the Sacramento-San Joaquin Delta. Leveraging the Youth-Focused Community and Citizen Science (YCCS) framework, the program connects youth to local ecosystems while addressing ecological challenges such as the Thiamine Deficiency Complex affecting Central Valley Chinook Salmon. The objectives focus on enhancing students' understanding of scientific concepts and processes, fostering science identity, self-efficacy, and environmental science agency, and cultivating a sense of environmental stewardship. Additionally, the program emphasizes the active involvement of community members in co-creating and refining educational strategies, ensuring these approaches are tailored to the diverse cultural and educational needs of the Delta community. This aligns with Science Action C under Management Need 4 in the 2022-2026 Science Action Agenda (SAA), contributing to a broader understanding of community-engaged research methodologies.
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.
The San Francisco Estuary (SFE) supports the southernmost reproductive population of longfin smelt (LFS) along the Pacific Coast. Long term monitoring studies have observed a precipitous decline of LFS in the SFE over the past several decades, and the San Francisco Bay-Delta Distinct Population Segment was listed as endangered under the Endangered Species Act in July of 2024. There are important gaps in our understanding of LFS ecology and movement within the highly urbanized SFE, posing challenges to the development of effective recovery strategies. More complete information about the movement and migration of LFS in the wild can lead to improved life-cycle modeling and provide insight into the species’ relationship with temperature, salinity and other habitat features of the SFE. An effective tool to learn about fish migration and movement is through a tracking method known as acoustic telemetry. Until recently this practice has been impossible on small fish such as LFS due to their body size relative to existing acoustic transmitters, or ‘tags’. With recent advances in telemetry technology, we now have an opportunity to implant newly miniaturized acoustic transmitters into adult LFS. However, before the results of telemetry studies utilizing these newly developed transmitters can be used to make inferences about wild populations, it is imperative to determine whether the tagged individuals are surviving and behaving in the same way as their un-tagged counterparts. The study aims to establish post-tagging survival and transmitter retention rates of wild and captive-reared LFS surgically implanted with newly miniaturizes acoustic transmitters, as well as the sublethal effects of transmitter implantation on LFS swimming performance. The results of this study will directly inform the implementation of acoustic telemetry on LFS, aiding in the conservation and recovery of an imperiled native species.
Little is known about sturgeon mortality sources outside management of the White Sturgeon recreational fishery. Mortality has been observed throughout the SFBDE with increased reporting over the past several years. Much of which is concentrated (but not exclusively) in the Carquinez Strait; a narrow strait linking known sturgeon feeding grounds and vital corridor which all SFBDE sturgeon must pass to access spawning grounds. Adult sturgeon populations in the SFBDE are difficult to estimate in part due to unknown rates of mortality, outside the recreational fishery. Specific, non-angling mortality data and sources are needed to develop management strategies that that lead to robust abundance estimates ensuring persistence of these public resources. This project aims to dentify and enumerate non-fisheries sturgeon mortality in the San Francisco Bay Delta Estuary (SFBDE), specifically the Carquinez Strait. We plan to determine population characteristics of observed mortality, age structure and migration patterns/habitat use of collected sturgeon. We will also engage the local community through outreach efforts to investigate the public perception of sturgeon mortality in SFBDE and increase participation in our study.
The Sacramento River and its tributaries serve as critical habitat for the green sturgeon, listed as federally threatened due to its declining population and the impacts of anthropogenic activities such as dam operations and water extraction. We currently lack an understanding of the relationship between flow regimes and sturgeon migration, which is essential for developing effective management strategies to support the species' conservation and for required analysis under state and federal law. By modeling this relationship, this project will contribute to more informed water management, leading to fewer litigation risks for agencies and better outcomes for sturgeon.
This project will model the effects of flow regimes on adult Southern Distinct Population Segment (sDPS) green sturgeon migration within the Sacramento River basin to enhance sturgeon conservation and water management. Specifically, the research will model how flows and temperature affect adult green sturgeon spawning migration. The model will be used to forecast sturgeon movements under various flow scenarios, and the model, the results, and an explanation of their significance will be widely distributed via a website (with a publicly accessible modeling app), a policy brief, a public workshop, and other outreach.
SacPAS serves to provide information integration services to the Central Valley Project Improvement Act and practitioners working on matters related to ESA-listed fishes. The web-based services relate fish passage to environmental conditions and provide resources for evaluating the effects of river management and environmental conditions on salmon passage and survival.
The work performed as part of this agreement includes developing, maintaining, and making accessible query tools and decision support tools to access: historical, real-time and forecasted data; data summaries and visualizations; and hindcasts, forecasts, and scenario-derived predictions from statistical and mechanistic models. More specifically, the objectives are to:
1) Maintain and extend a secondary data repository of historical, real-time, and forecasted fish, environmental, and operational data from the Sacramento River and other river systems in the Central Valley, integrated from primary, public databases.
2) Maintain and improve the data query and visualization tools and services provided through the SacPAS website (https://www.cbr.washington.edu/sacramento/) for historical, real-time, and forecasted environmental and fish data.
3) Conduct research and provide access to modeling tools for fish survival and migration, through the SacPAS website, in support of Reclamation-funded and ESA-mandated activities, especially in efforts to predict, track, and evaluate the efficacy of proposed or actual actions.
Chinook Salmon (Oncorhynchus tshawytscha) populations in California are in decline due to the combined effects of habitat degradation, water diversions, and shifting climate regimes. This project uses archival tissues (otoliths, vertebrae) from modern and ancient spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.
The Wetland Regional Monitoring Program (WRMP) Fish and Fish Habitat Monitoring project is a collaborative effort to track biological responses to tidal wetland restoration in the San Francisco Estuary. Monthly sampling is conducted across a network of benchmark, reference, and project restoration sites in the South Bay and North Bay, with the goal of evaluating how wetland restoration influences fish assemblages, habitat use, and ecological condition.
The study uses primarily otter trawls to monitor fish and macroinvertebrate communities. Standardized field methods align with those used in long-term monitoring programs to ensure comparability and data integration across regions. Environmental data, including water temperature, salinity, and dissolved oxygen, are collected in tandem with biological sampling to assess habitat quality and seasonal dynamics.
The program addresses WRMP Guiding Question #4: How do policies, programs, and projects to protect and restore tidal marshes affect the distribution, abundance, and health of fish and wildlife? The data support adaptive management, regulatory compliance, and science-based restoration planning by identifying key habitats, tracking restoration performance, and detecting regional patterns in species composition and abundance over time.
