Science activities

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 work will model the risk of pesticide pollution in 225 sub-catchments of the Sacramento-San Joaquin Bay-Delta. The model will account for water management practices, land use, pesticide use rates, and cumulative pesticide stress. Additionally, this work will produce a web-based tool to simulate current and future risks based on the ranking of primary sources of pesticide contribution. This work will provide a framework to predict risk from chemical stressors. Specific objectives are: (1) enhanced pro-active chemical risk assessment, (2) creation of a tool which enables science-based chemical use decisions, (3) improved risk screening for vulnerable areas, and (4) identification of adverse effects of current and future chemical use strategies.

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.

The San Joaquin County & Delta Water Quality Coalition was established to help irrigated agriculture meet the requirements of the California Regional Water Quality Control Board's (RWQCB) Irrigated Lands Regulatory Program (ILRP) in San Joaquin County, Calaveras County and Contra Costa County. The Coalitions is operated and governed by the San Joaquin County Resource Conservation District. Under the ILRP that was originally adopted in July of 2003, farmers and ranchers that irrigate their land and have runoff from that irrigation or rainfall must belong to a coalition or apply for an individual discharge permit from the Regional Board directly.

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).

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.

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 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. 

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.

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.

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:

• Unified access to quality-controlled, time-series water data;
• Enhanced spatial visualization and modeling capabilities;
• Improved collaboration among agencies and stakeholders through shared tools and insights.

This work will support more informed decision-making and help ensure the long-term safety, reliability, and ecological integrity of California’s water resources.

Assessing fire retardant toxicity on salmonids (eggs and alevins).