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.
The federal hatcheries mark and tag fish that are released into the river or bay using a combination of coded wire tags (CWT) and adipose fin clipping. The number of fish tagged and the identifiers are reported to the RMPC which is part of the RMIS. The Regional Mark Processing Center (RMPC) provides essential services to international, state, federal, and tribal fisheries organizations involved in marking anadromous salmonids throughout the Pacific region. These services include regional coordination of some tagging and fin marking programs, maintenance of databases for Coded Wire Tag Releases, Recoveries, and Locations, as well as the dissemination of reports of these data in electronic or printed form when requested. These databases are known collectively as the Regional Mark Information System (RMIS).
The overarching AIS goal is that "Risks of aquatic invasive species invasions are substantially reduced, and their economic, ecological, and human health impacts are minimized. This goal is addressed through a series of performance and workload measures. The AIS Program provides funding for Aquatic Invasive Species Coordinators for each Region within the Service and their respective aquatic nuisance species activities. These coordinators work closely with the public and private sector to develop and implement invasive species projects. One of the primary initiatives of the program is the prevention of invasive species via boats through the "100th Meridian Initiative" (overseen by individual AIS regional coordinators). This initiative aims to prevent the spread of aquatic invasive species by boats personal watercraft and other pathways. Through boat inspections and boaters assessments along the 100th meridian, partners can learn how to prevent the spread of zebra mussels and other AIS via transport of boats and personal watercraft.
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.
The Environmental Monitoring Program (EMP) has conducted the Zooplankton Study since 1972 to better assess trends in the lower trophic food web in the San Francisco Bay-Delta estuary. The study also detects and monitors zooplankton recently introduced to the estuary and determines their effects on native species. Under the auspices of the Interagency Ecological Program for the San Francisco Estuary and mandated by Water Right Decision D-1641, the EMP Zooplankton Study is part of the Environmental Monitoring Program and is conducted by the California Department of Fish and Game (CDFW), California Department of Water Resources (DWR), and the United States Bureau of Reclamation (USBR).
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.
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.
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 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.
Managing California’s water supply is complex, requiring careful coordination to ensure sustainability, water quality, and the protection of public and environmental health. In the Sacramento–San Joaquin Bay-Delta, hundreds of datasets from studies and monitoring programs are used to assess conditions and inform key operational decisions. However, these datasets are often fragmented across agencies and stored in inconsistent formats, making it time-consuming for analysts and researchers to locate and use the data effectively.
This project aims to enhance the Bay-Delta Live (BDL) data management platform (www.baydeltalive.com) by integrating datasets from the California Department of Water Resources’ Water Data Library (WDL). The primary focus is on water quality and environmental monitoring data. By streamlining access to these resources, the project will improve the discovery, retrieval, and analysis of water-related datasets across multiple sources.
Key outcomes include:
This work will support more informed decision-making and help ensure the long-term safety, reliability, and ecological integrity of California’s water resources.
