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.
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.
