Much research in the Delta has focused on foodweb dynamics, stimulated by evidence that low productivity of plankton is linked to declines in several fish species including the endangered delta smelt. Pseudodiaptomus forbesi is the most abundant copepod (small crustaceans) in the Delta in summer. It is an important food source for many fishes and makes up about half of the food of delta smelt. This study focuses on the feeding, reproduction, and growth of copepods as essential foodweb support for fishes. This work investigates four diverse habitats including two open-water channels and two shallow habitats. The researchers will measure copepods' feeding rates on microscopic plants and animals, and relate feeding to their rates of growth and reproduction. Computer models will be used to estimate their movement and death rates. These results will show the sources of nutrition used for growth and reproduction of these key organisms. Results will inform how food webs respond to large scale changes in the Delta ecosystem, for example, restoration and the Sacramento wastewater treatment plant upgrade.
In June 2004, a 350-foot levee section gave way west of Stockton, flooding crops and more than a dozen homes, and challenging state officials to protect the state's water supply. What is the risk of that happening again somewhere in the Delta? In light of agricultural fields sinking, the sea level rising, more frequent and severe floods occurring, and earthquakes looming, improvements are estimated to cost $3.8 - $4.3 billion over the next few decades. This study combines 3-D representations with information on the levee's structure to analyze how different levees respond to floods, sea level rise, and earthquakes. State officials released the last Delta Risk Management Strategy a decade ago. Since then, scientists have collected significant amounts of data and have developed new procedures to compute the risk of failure. This work will produce new Delta-wide data sets important for characterizing the hazards coming from floods and earthquakes. It will also develop the best method to conduct levee hazard assessments. Applying this new method will ensure wise investments and effective threat mitigation Delta-wide.
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.
This study combines detailed model predictions with salmonid tracking data to inform how river flows affect steelhead movement through the Delta. This project leverages an existing 6-year data set to support analysis of salmonid behavioral responses across a broad range of water years. The study will evaluate behavior relative to flow under existing regulatory requirements (Old and Middle River Flow and the Inflow to Export ratio), evaluate five new potential water management metrics identified by the Collaborative Adaptive Management Team Salmonid Scoping Team, and improve the understanding of what conditions affect survival.
The decline of native salmon species has resulted in their protection under the U.S. Endangered Species Act and the California Endangered Species Act. Disease and predation are primary drivers of mortality as salmon migrate. Multiple stressors, such as exposure to contaminants and elevated temperature, can impact rates of disease and predation of salmon as they migrate to the ocean. This study examines how contaminant exposures at different temperatures affects salmon health. Specifically, the study investigates the sensitivity of salmon to a contaminant mixture of bifenthrin (a pyrethoid pesticide) and triclosan (an antibacterial added to personal care products). Both contaminants can alter fish swimming behavior and critical physiological functions. Similarly, temperature stress can impact fish physiology and behavior, as well as exacerbate the adverse effects of contaminants.
To support management planning in Suisun Marsh, this project is developing a body of science and tools to understand past, present, and potential future changes to the Marsh’s ecological patterns, processes, and functions. This project builds on SFEI’s prior work in the Delta, extending historical ecology mapping, landscape change studies, and the Landscape Scenario Planning Tool to cover Suisun's historical and present-day landscapes. Through spatially explicit representations of the historical function and condition of the marsh and analyses of landscape metrics, this project is evaluating changes over time in landscape support for ecosystem functions and services in Suisun. In order to incorporate diverse perspectives into planning resources, project activities include engagement with local tribes and community members to understand community interests, priorities, and uses of the Marsh. Findings will be shared through a report and article for both technical and general audiences, and spatial analyses and data layers will be made available through the Landscape Scenario Planning Tool.
On-going subsidence of organic soils threatens the physical structure of the Delta, its central role in the state’s water system, many diverse species that depend on it, and threatens future agricultural production. Knowledge of baseline emissions and subsidence rates is important for developing alternative land use scenarios for maximizing benefits for sequestering carbon, reducing or reversing subsidence, providing income for landowners via the carbon market, and reducing flood risk. This project will gather, process, and analyze recent data in the Delta for land-surface elevation changes, greenhouse gas fluxes measured by eddy covariance and gas chambers, soil organic matter content, depth-to-groundwater, and soil organic thickness. These data will be used to update and calibrate the SUBCALC model and refine model inputs to improve the model’s ability to simulate subsidence and CO2 emissions. Collaboration with the Jet Propulsion Laboratory and UC Berkeley will allow use of CO2 flux and InSAR data to calibrate and validate the SUBCALC model. The Delta Conservancy is another partner assisting with assessment of modeling for land-use conversion planning. TNC and Metropolitan Water District are partners to assist with use of SUBCALC for engagement of the carbon market and collaborate with the Suisun RCD to improve estimates of subsidence and CO2 emissions.
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.
The Sacramento-San Joaquin Delta (Delta) is experiencing an increase in the frequency and severity of Cyanobacterial Harmful Algal Blooms (CHABs), which can produce harmful cyanotoxins. This issue is likely to intensify due to climate changes and rising temperatures. The most common CHAB genus in the Delta is Microcystis. Currently, the most extensive dataset for tracking Delta CHABs is the Microcystis Visual Index (MVI), a qualitative assessment of Microcystis colony densities observed in surface water. This index, recorded by natural agency staff across numerous monitoring stations, provides broad spatial coverage but is inherently subjective and not quantitative, thereby limiting its utility.
This project has the following objectives: 1. Develop an MVI image classification model and model algorithm that can identify and quantify Microcystis aggregate presence and coverage level in digital photos. 2. Translate MVI rankings to Microcystis biomass ranges by obtaining data to ground-truth a range of Microcystis biomass that corresponds with MVI rankings 2 through 5. 3. Explore relationship between proportion of toxic Microcystis cells and Microcystis biomass levels by relating each MVI scale (for ranks 2 through 5) and Microcystis biomass range to a) proportion of toxic Microcystis cells (i.e. ratio of mcyE and 16S rDNA genes) and b) microcystin concentration, in surface grab samples.
(The photo is a drone view of an algal bloom in San Luis Reservoir in September 2024. Credit: The California Department of Water Resources.)
Assessing the success of tidal marsh restoration is a top priority for coastal managers across the US. Estuarine habitat restoration has been prioritized due to the importance of the ecosystem functions (Callaway et al. 2012) and services (Costanza et al. 2014) they provide and the threats to them by climate driven sea-level rise (hereafter SLR; Craft et al. 2009, Donnelly & Bertness 2001, Schile et al. 2014) and other stressors (Mariotti & Fagharazzi 2013). Given the importance of management for estuarine habitats to survive SLR (Kirwan & Megonigal 2013) and the importance of public responses to approve and fund restoration projects, it is critical to understand how to broadly assess the success of restoration from the perspectives of both ecological performance and public perceptions. However, the San Francisco Estuary (SF Estuary), stretching from the Lower San Francisco Bay through Suisun Marsh to the Sacramento-San Joaquin Delta, encapsulates diverse social and environmental dynamics (Moyle et al. 2014) and varying perceptions by sociodemographic group (Rudnick et al 2022). Our project is focused on the Suisun Marsh and Delta and seeks to understand these complexities by integrating social, environmental, and management perspectives.
The Eco-Cultural Renewal of Delta Tule Landscapes project is a collaboration between the San Francisco Estuary Institute (SFEI) and two Delta area Tribes: the Shingle Springs Band of Miwok Indians (SSBMI) and the Colfax Todds Valley Consolidated Tribe (CTVCT). This project's goals are to communicate the central importance of Traditional Ecological Knowledge (TEK) in creating and maintaining resilient Delta landscapes and to advance the integration of TEK into Delta science, management strategies, and policies in a way that supports the ecological and cultural value of the Sacramento-San Joaquin Delta, a region of profound ecological and cultural significance. TEK is the evolving knowledge acquired by indigenous peoples over hundreds or thousands of years through direct contact with the environment. In the Delta, Tribes used TEK to tend wetlands and foster abundant populations of the plants and animals they harvested. This project aims to elevate TEK in the Delta as an essential tool to restore and build the resilience of species, habitats, and ecosystem processes that have been devastated since European
Decisions over how water is allocated consider a limited range of climate and operational scenarios, privilege Western knowledge, and are generally inaccessible to the public, including communities most affected by water decision-making. We will follow a participatory and iterative co-production process to understand and integrate the diverse values and uses of Delta waterways and floodplains in an accessible knowledge platform designed to promote public engagement, learning, and equitable stewardship.
The overarching goal of the proposed project is to build and integrate knowledge of the social-ecological uses of Delta waterways and floodplains to inform equitable solutions to Delta management challenges. Specific objectives are to (1) understand the diverse public beneficial uses Delta waterways and floodplains; (2) incorporate functional flows and riparian floodplain processes in Delta water operations models; (3) share diverse community knowledge through a web-based platform; and (4) critically evaluate our collaborative research approach to assess its efficacy in building trust, enhancing public engagement, and guiding equitable stewardship actions.
As source areas of snowmelt, Sierra Nevada headwater streams are the origin of water that feeds the Delta, but their response to climate change is not well understood. By utilizing long-term data and modeling future responses, we build a tool to reduce scientific uncertainty about Delta water supply and water quality in a changing climate. By incorporating indigenous cultural values, we create a fully integrated shared vison of the future of the Delta in a changing climate, including mapping which areas are most vulnerable and in need of conservation or restoration.
The project objectives are: 1. Utilize and expand on existing water quality and biological monitoring networks in Sierra Nevada headwaters streams to construct models of ecosystem dynamics with respect to climate induced stress impacts on benthic communities, water quality, and nutrients. 2. Construct an oral-history-derived framework of indigenous cultural values of Delta headwaters systems and how science and indigenous values can interact to improve management outcomes. 3. Utilize and expand on existing platforms for dissemination of forecasting tools and model outputs to water managers as well as both scientific and non-scientific communities in the Delta headwaters.
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 Sacramento-San Joaquin Delta (Delta) faces a serious threat from the recent proliferation of cyanobacterial harmful algal blooms (cyanoHABs), particularly due to the production of high levels of cyanobacterial toxins. These blooms jeopardize water quality and pose a significant risk to air quality when toxins are released as particles in a process known as aerosolization. When people inhale these aerosols, it can trigger an inflammatory response, yet the specific form in which toxins are aerosolized remains unknown. Thus, an improved understanding of cyanobacterial toxin aerosolization mechanisms has significant human health implications. To assess the public health risks associated with airborne cyanobacterial toxins, the project examined the size distribution of cyanoHAB aerosols and the factors influencing their aerosolization. They also investigated the role of nutrient enrichment in cyanoHAB growth, cyanobacterial toxin production, and cyanotoxin aerosolization through a combination of laboratory and field experiments.
Project Objectives
1. Investigate and quantify the production of primary spray aerosols during cyanoHABs
2. Assess the linkage of nutrient enrichment, phytoplankton community composition, toxin production, and cyanoHAB aerosol formation
This project addresses a pressing environmental and public health concern. The data can be used to protect vulnerable communities living near affected bodies of water and inform ways to mitigate the adverse impacts of cyanoHABs on the Delta’s environmental and public health.
This research improves Delta-specific human exposure guidelines to cyanoHAB aerosols by providing data essential for implementing effective public health measures, including recommendations on mask usage and understanding the expected way aerosols travel through the air from the shoreline. Their investigation into the relationship between nutrient availability, cyanoHABs growth dynamics, toxin production, and aerosol formation will offer valuable insights for management efforts aimed at regulating algal blooms to improve both water and air quality outcomes. Ultimately, this research will strengthen state agency responses to human illness associated with cyanoHABs and toxin exposure.
Cyanobacteria are the most common plankton causing harmful algal blooms in freshwater. The variety of cyanotoxins produced by cyanobacteria can impact the nervous system, liver, gastrointestinal tract, respiratory system, and skin of humans and other animals. In the Sacramento-San Joaquin Delta (Delta), cyanobacterial harmful algal blooms (cyanoHABs) have become more prevalent since the late 1990s. Even with the welldocumented occurrence of cyanoHABs in the Delta over the last 15 years, there is no consistent monitoring program in the region, making it challenging to identify management actions to mitigate their occurrence and effects.
To fill this knowledge gap, this project focused on measuring cyanotoxins and cyanoHABs in the Delta, organizing relevant data for stakeholders, and synthesizing data about cyanoHAB extent and drivers. In addition to the generation of new data, this project developed tools to integrate existing and future data collection efforts. Synthesis of these data will help assess the status and trends of cyanoHABs in the Delta, elucidate factors contributing to bloom formation, cyanotoxin production, and transport, and ultimately better understand the effects of cyanoHABs on humans, other animals, and the ecosystem.
Salmon of California’s Central Valley are culturally and ecologically valuable but are subject to numerous stressors.
This project used sociological and ecological methods to address salmonid recovery in the Central Valley in an inclusive and collaborative way. The research team identified a suite of implementable and impactful actions that will advance the recovery of Central Valley salmon and steelhead. The approach promoted broad buy-in for these preferred actions by making trade-offs transparent and balancing participants’ diverse values, perspectives, and priorities.
Spring-run Chinook salmon (Oncorhynchus tshawytscha) are a high-priority species under the Endangered Species Act due to their risk of extinction. However, understanding the factors affecting their populations is difficult when monitoring focuses only on returning adult spawners. This limited view overlooks critical life stages. To address this gap, the project aimed to estimate the number of juvenile salmon leaving the Delta at Chipps Island. Monitoring salmon throughout their entire life cycle is essential for identifying the key factors influencing their survival and reproduction.
There is a need from both scientists and managers for accurate data to make informed decisions about salmon protection and conservation. The Department of Water Resources (DWR) mandates that juvenile production estimates for spring-run salmon be included in their incidental take permit, which is necessary for the continued operation of the State Water Project. A method to estimate juvenile abundance of spring-run salmon leaving the Delta (at Chipps Island) did not yet exist.
To develop these annual estimates, researchers built on previous studies and incorporated new genetic data into updated models. This approach maximized the use of available information and the latest genetic research to improve the protection and understanding of these threatened fish.
This project examined cold water storage and regulation in Shasta Lake through the Shasta Dam Temperature Control Device (TCD). The TCD is a 300-foot structure with multiple gate openings, allowing water from different depths - and thus different temperatures - to be selectively released to manage water temperature in the river downstream. River water temperature is managed to support the imperiled Chinook salmon, a species of fish that is native to California. This capability is becoming increasingly important because low water years generally mean warmer river water temperatures that compromise habitat suitability for different species. In particular, cold pool management is essential for downstream spawning and rearing habitat for winter-run Chinook salmon that rely on cooler water temperatures to survive and reproduce. When the water is too warm, oxygen availability is limited for Chinook salmon and their eggs, which contributes to their mortality. Although the TCD allows reservoir managers to control water release and downstream water temperature, flow contributions into the TCD under day-to-day operations for different gate openings, operations, and thermal conditions within the reservoir are largely unquantified. Further complicating temperature management, TCD leakage (whether within the structure itself or through malfunctioning gates) needs to be better quantified in location and magnitude. This information will improve operational strategies for cold water performance especially during summer and fall months to manage cold water supply for downstream Chinook salmon habitat.
