Science activities

This project aims to quantify the impacts of common reed (Phragmites) invasion on community structure and ecosystem function during early stages of tidal restoration in wetlands. The study will focus on the Tule Red Tidal Restoration site in Suisun Marsh. The research aims to produce a conceptual model that will describe habitat structure, invertebrate communities, and predator use of wetlands affected by Phragmites invasion. The conceptual model resulting from this study will guide future predictions of wetland response to invasion and to develop mitigation strategies. Data collected will also support food web models and the understanding of invasive plants as stressors, as well as foster translational science to the management community.

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.

Pesticide and nutrient inputs from human activities are present in the Sacramenot-San Joaquin Bay-Delta, but the impact of these stressors together on algae is not well known. This research will examine the impacts of herbicides and nutrients on the growth and stress responses of phytoplankton and cyanobacteria present in the San Francisco Estuary. The algae in the delta are diverse with critical ecological effects, ranging from toxin-producing cyanobacteria that form hazardous algal blooms to benthic diatoms and green algae that make up the bulk of the aquatic food web. Contaminants and herbicides can cause changes in algae cellular health which may impact population growth. Understanding algal sub-lethal stress responses will improve our understanding of stressors on the bay-delta food web and bloom formation.

This project aims to improve understanding of atmospheric and hydrologic carbon fluxes in a restored tidal salt marsh in the South San Francisco Bay. I will use soil chambers to measure how much carbon dioxide and methane is taken in and emitted from the marsh. The project will also examine how spatial variability in marsh surface cover impact these exchanges. Shahan will use the data collected in this study to create a biogeochemical model that estimates the carbon budgets of wetlands in the Bay-Delta. A complete carbon budget will illuminate relationships between carbon fluxes and environmental variables. This information can support more informed management of wetlands, as well as allow researchers and decision makers to more effectively plan wetland restoration to be effective in managing carbon fluxes in the face of possible impacts due to climate change.

This project aims to characterize and quantify where detrital material (decaying plant matter) originates within wetlands, the composition of that material, and how export of detrital particles occurs. This project will combine powerful characterization tools and techniques that scale from molecules to ecosystems to assess spatial and temporal trends in particle sources, species and composition. Because restoration in the Sacramento-San Joaquin Delta will fundamentally alter particle distribution and food availability for aquatic organisms, this study will inform habitat restoration efforts and the revival of native fish populations. The tools developed and adapted for this project may inform management response during extreme conditions and climate events by helping to identify areas that may act as refugia for species.

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 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 Environmental Monitoring Program (EMP) began in 1975 to conduct baseline and compliance monitoring of water quality, phytoplankton, zooplankton, and benthic invertebrates in the San Francisco Bay-Delta estuary. This monitoring program was designed to track the impact of water diversions to the State Water Project (SWP) and Central Valley Project (CVP) on the Bay-Delta. In the decades since, EMP scientists have monitored these constituents at fixed and floating stations throughout the estuary and ensured compliance with state and federal mandates such as Water Right Decision 1641 (D-1641). In the years and decades since its inception, EMP has become one of the cornerstones for scientists' and managers' understanding of the pace and pattern of change in this critical ecosystem. By sampling water quality and biological communities concurrently, EMP has created a dataset that is uniquely useful in better understanding causal connections between physical, biological, and biogeochemical processes. 

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 Sacramento-San Joaquin Delta is a highly altered and impaired ecosystem that is critical to the freshwater infrastructure of the State of California. Salt intrusion from San Francisco Bay into the Delta, however, threatens freshwater delivery to the southern portions of the state and so management and restoration actions within the Bay-Delta must continuously balance both ecosystem and operational needs. While previous  numerical modeling studies have sought to examine changes in the estuarine physics of the system, these tools are costly to develop and run. Thus there is a need to develop alternate methods for monitoring the movement of water through the Bay-Delta, as proposed here. The proposed research project approaches tracking the mixing between the Bay and Delta waters through the novel use of daily satellite color imagery. These findings will be linked to in situ measurements throughout the system and used to inform relevant agencies of flow characteristics within the waterways. This work is motivated by a need for high frequency monitoring of finescale features within the dynamic Bay-Delta ecosystem and to take advantage of new advanced remote sensing technology to inform on long-term trends within the Delta.

The primary objectives of this research are to: 1. Enhance monitoring programs to inform management in the presence of climate change and additional stressors, 2. Inform on ecosystem resilience to interannual hydrologic variations and climate change impacts, and 3. Evaluate how climate change and flow regime changes will impact water quality in the Delta.

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.

Invasive aquatic vegetation (IAV) is widespread in the Sacramento-San Joaquin Delta (Delta) and its change in coverage has been mapped at the species level using spectroscopy data collected once a year, from 2004 to 2008 and from 2014 to 2019. There was no funding to conduct a similar mapping campaign in 2020. This work aims to collect and analyze imagery in summer of 2020 to fulfill two main objectives. First is to inform the monitoring framework for aquatic vegetation put forth for the Interagency Ecological Program (IEP). Comparing spring and fall imagery of 2019 and the summer imagery of 2020, the project will evaluate which time period is ideal for optimal mapping of aquatic vegetation considering the logistical challenges of airborne imagery acquisition and the phenology of the species being mapped. The project will also contrast the pros and cons of the 3 proposed scenarios in the IEP monitoring framework: 1) two hyperspectral acquisitions a year (2019; “best case” scenario), 2) one acquisition a year (2020, “moderate” scenario) and 3) satellite
data based monitoring (the Sentinel-2 study, “bare bones” scenario). The second objective of the project is to determine if the new treatment framework (new herbicide formulations and application schedules) is effective in controlling the old (Brazilian waterweed, water hyacinth) and newly added target weed species (water primrose, alligator weed) in the Delta ecosystem. 

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.
 

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.