Our Program and Focus Areas

Water Quality Science Informing Stewardship

SFEI’s Clean Water Program is one of the nation’s premier water quality science programs. It anticipates and meets the water quality data needs of policy-makers, resource managers, and the public. It helps the public, regulators, and those who discharge into our waters create more effective policies to ensure the health of our waters. The Clean Water Program consists of several programs and initiatives:

  • The Regional Monitoring Program for Water Quality in San Francisco Bay (Bay RMP) — Now in its 22nd year, the RMP is the flagship of the Clean Water Program. The RMP is a model program to present decision makers with the best available science on pollution in San Francisco Bay. The RMP combines high quality science, forward planning, public forums, and the delivery of clear and actionable data to watershed managers and the public.
  • SFEI has helped develop the Delta RMP to inform better policy-making for Delta water quality, and is about to begin the first year of monitoring. As with its Bay-focused predecessor, the Delta RMP will provide the science to drive lower-cost, more efficient and effective regulations. This science will benefit the Delta’s many users, from farmers to fisherman, boaters to residents.
  • SFEI is the scientific lead for the San Francisco Bay Nutrient Strategy, to address the most complex and costly issue confronting the wastewater treatment community since the Clean Water Act mandated secondary treatment 40 years ago.
  • Our Green Chemistry research fills critical needs of agencies involved in efforts to prevent pollution by advising manufacturers about safer options.
  • The Green Infrastructure initiative provides scientific support and innovative tools for long-term planning of water infrastructure upgrades to achieve green alternatives, improved water quality, and sustainability.
 

For more information on the SFEI Clean Water Program, please contact Program Directors Jay Davis, Ph.D. and David Senn, Ph.D.

Events and Meeting Materials

 

The Bay Regional Monitoring Program (RMP) provides water quality regulators and policy-makers with information they need to manage the Bay effectively. The RMP is an innovative collaborative effort between SFEI, the Regional Water Quality Control Board, and the regulated discharger community. The Program was established in 1993, and has an annual budget of $3.5 million.

 

RMP Manager: Melissa Foley   Lead Scientist: Jay Davis

 

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Pollutants that accumulate in the food web (or “bioaccumulate”) are impairing the health of aquatic ecosystems throughout California. Methylmercury bioaccumulation is a particularly widespread and severe problem, and poses a serious threat to human and wildlife health across the state. Monitoring information will provide an essential foundation for control plans and exposure reduction plans to remedy bioaccumulation problems in California water bodies. In addition, effective communication of this information to the public is imperative to enable fish consumers to reduce their exposure to pollutants.

However, California still lacks the comprehensive monitoring, assessment, and communication needed to adequately support management of bioaccumulative pollutants in California water bodies. There are multiple problems with the status quo:

  • insufficient information on spatial extent and long-term trends, high priority topics such as contaminants of emerging concern (CECs) and biotoxins, and the relative importance of different sources and environmental factors that drive bioaccumulation;
  • inefficiencies due to a lack of coordination between agencies, and between agencies and regulated entities;
  • a need for pilot scale actions to reduce bioaccumulation accompanied by refinement of monitoring tools to track the effectiveness of the actions;
  • safe eating guidelines are needed for many additional water bodies, but the current pace of development is slow due to funding limitations,
  • a need for optimizing the effectiveness of communication to the public in support of exposure reduction, and
  • insufficient access to data and information for regulators, scientists, and the public.

Efficient use of the limited funds available for monitoring, assessment, and communication is of paramount importance. This efficiency can be achieved through close coordination of programs and thoughtful strategic planning. California needs a central entity with the responsibility and authority to convene a forum to attain the degree of coordination and cooperation that is required to address the bioaccumulation problem. The Bioaccumulation Oversight Group (BOG) has been established as a work group of the California Water Quality Monitoring Council to fulfill this role. A Strategy for Coordinated Monitoring, Assessment, and Communication of Information on Bioaccumulation in Aquatic Ecosystems in California has been prepared by the BOG to outline steps that should be taken to improve bioaccumulation monitoring, assessment, and communication in California.

SFEI acts as the scientific lead for developing and implementing the Bay’s Nutrient Management Strategy. In this role, SFEI staff work with teams of regional scientists to develop the necessary scientific understanding to allow regulators and stakeholders to make informed decisions about i) whether the Bay is trending toward nutrient-related impairment; ii) what nutrient reductions are needed to mitigate or prevent impairment; and iii) sub-regional and regional approaches that achieve necessary reductions and yield the highest ratios of overall benefits to cost.

Overview:

San Francisco Bay receives high anthropogenic loads of the nutrients nitrogen and phosphorous - higher than many other US estuaries that experience nutrient-related water quality impairments such as excessive algal blooms, low dissolved oxygen and fish kills, and blooms of toxin-producing algae. Until recently, the Bay was considered to have innate strong resistance to high nutrients. However, recent observations suggest that the Bay is experiencing a “regime shift” toward higher sensitivity to nutrients. The Bay’s true trajectory is cloaked in uncertainty. One plausible scenario is that the Bay’s current level of resistance will be maintained and no further degradation will occur. Another equally plausible scenario is that the Bay’s resistance to nutrients will continue to decline until moderate to severe impairment occurs in some subembayments.

Treated wastewater from the Bay Area’s 42 publicly owned treatment works (POTWs) is a major nutrient source Bay-wide. Waters entering the Bay from the heavily-farmed Central Valley act as another large nutrient source that disproportionately influences the northern Bay. Upgrading POTWs to substantially decrease nutrient loads will come at enormous public expense: $2-10 billion. That expense is undoubtedly justified if nutrients are indeed causing (or will eventually lead to) impairment, and if reducing POTW loads will mitigate or prevent that impairment. However, the scientific foundation needed to explore those issues needs to be developed.

Bay Area POTWs describe nutrients as the most complex and costly issue confronting them since the Clean Water Act mandated secondary treatment 40 years ago. Regulators and dischargers are highly engaged and seeking alignment. In that sense, nutrients also represent an enormous opportunity: a catalyst for sub-regional and regional water and wastewater planning to achieve multiple long-term objectives.

Projects Related to the Clean Water Program

The Pulse of the Bay

https://www.sfei.org/documents/2019-pulse-bay-pollutant-pathwaysDownload the Pulse of the Bay! This report from the Regional Monitoring Program for Water Quality in San Francisco Bay features articles on the four major pathways by which pollutants enter the Bay: municipal wastewater, industrial wastewater, stormwater, and dredging and dredged sediment disposal.  Each article provides a basic introduction to the pathway and discusses the regulatory framework, recent findings, and future challenges.  The report also includes some of the latest highlights from monitoring of important parameters such as nutrients, emerging contaminants, mercury, PCBs, and selenium.    

Sediment Solutions

Sediment Solutions is a timely and innovative project that builds on SFEI’s past work, operationalizing cutting-edge science to inform management approaches that take advantage of natural processes to provide more creek sediment to baylands, increase climate resilience, and enhance creek health. With study areas in North Bay, East Bay, and South Bay, the project will provide new guidance for management strategies that support flood risk management and ecosystem health benefits throughout the region.

Statewide Plastics Monitoring Plan & Strategy

Plastics, in their various chemical composition and sizes, pose serious challenges to the vitality of California's ecosystems. Once escaped into the environment, plastic contamination persists for very long periods and breaks down into ever smaller pieces, becoming more readily available to wildlife and populations who live, work, and play in those same habitats.

RMP Update

The Regional Monitoring Program for Water Quality in San Francisco Bay is an innovative collaboration of the San Francisco Bay Regional Water Quality Control Board, the regulated discharger community, and the San Francisco Estuary Institute. It provides water quality regulators with the information they need to manage the Bay effectively. The RMP produces two types of summary reports: The Pulse of the Bay and the RMP Update. The Pulse focuses on Bay water quality and summarizes information from all sources.

Next Generation Urban Greening

SFEI is working with partners across the Bay Area to design tools to help cities achieve biodiversity, stormwater, and climate benefits through multifunctional green infrastructure.

California Pesticides: A Data Visualization Tool to Link Pesticide Use and Management to Water Quality

Despite California's data-rich environment, there are still many obstacles when trying to access and understand pesticide data at the nexus of water quality, ecological effects, and human health. We recognize a need to fill data gaps, not necessarily by collecting new data, but by better leveraging information already technically in the public domain. The goal of this project is to bring pesticide reporting, occurrence, and toxicity data together in ways that yield insights and meet the expressed needs of stakeholders in clear, efficient, credible, and repeatable ways.

Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS)

A recent analysis of PFAS in the surface waters of SF Bay was conducted to understand the occurrence, fate, and potential risks to ecological and human health. Eleven of 40 PFAS were detected at part per trillions (ppt) concentrations in ambient water collected in 2021 from 22 sites in the Bay. Seven PFAS (PFPeA, PFHxA, PFHpA, PFOA, PFBS, PFHxS, and PFOS), were found in at least 50% of samples. Concentrations of PFAS in the Bay were generally consistent with similar studies globally for surface water. Sustained, multi-matrix monitoring of this important class of contaminants of emerging concern is a high priority for the RMP.

Microplastic Pollution in San Francisco Bay

Plastic pollution is gaining global recognition as a threat to the resilience and productivity of ocean ecosystems. However, we are only just beginning to understand the scope and impacts of microplastic particles (less than 5 mm) on coastal and ocean resources, and the San Francisco Bay Area is no exception. A preliminary study of nine water sites in San Francisco Bay, published in 2016, showed greater levels of microplastics than the Great Lakes or Chesapeake Bay.

Regional Watershed Spreadsheet Model

The Regional Watershed Spreadsheet Model (RWSM) was developed to estimate average annual regional and sub-regional scale loads for the San Francisco Bay Area. It is part of a class of deterministic empirical models based on the volume-concentration method.

RMP Annual Meeting

The 28th RMP Annual Meeting was hosted on Thursday, October 14th, 2021. Fully virtual for the second year, the meeting included an excellent lineup with presentations from RMP staff and other invited experts.  We heard about and discussed findings on Bay sediment supply, PFAS, tire particles and chemicals, and contaminants in Bay fish, among other topics. If you missed the meeting or any specific sessions, recordings of the meeting and presenter slides will be posted below shortly

Publications related to the Clean Water Program

The Institute has collectively produced more than 1300 reports, articles, and other publications over the course of its 24-year existence. The following list represents those publications associated with this individual program and its focus areas.

Year of Publication: 2024

Trinh M. 2021 Update to Copper Rolling Average. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1164.  (556.45 KB)
Trinh M. 2021 Update to Cyanide Rolling Averages. Richmond, CA: San Francisco Estuary Institute; 2024 .  (552.88 KB)
Yee D, Wong A, Weaver M. 2024 Quality Assurance Program Plan for The Regional Monitoring Program for Water Quality in San Francisco Bay. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1169.  (4.07 MB)
Paterson K, Miller E, Lin D. Microplastics Monitoring and Science Strategy for San Francisco Bay 2024 Revision. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1144.  (818 KB)
Avellaneda PM, Zi T. Modeling Stormwater Loads of Contaminants of Emerging Concern: Literature Review and Recommendations. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1131.  (468.55 KB)
Kleckner A, Davis J. Multi Year Plan 2024. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1167.  (3.3 MB)
Foley MM, Davis JA, Buzby N. Selenium Concentrations in Water and Clams in North San Francisco Bay, 2019-2020. Richmond, CA: San Francisco Estuary Institute; 2024 . Report No.: 1116.  (970.15 KB)

Year of Publication: 2023

Mendez M, Kleckner A, Sutton R, Yee D, Wong A, Davis J, et al.. 2023 Bay Prey Fish and Near-field / Margins Sediment Sampling and Analysis Plan. Richmond, CA: San Francisco Estuary Institute; 2023 . Report No.: 1141.  (406.78 KB)
Kleckner A, Sutton R, Yee D, Wong A, Davis J, Salop P. 2023 RMP Dry Season Water Cruise Plan. Richmond, CA: San Francisco Estuary Institute; 2023 . Report No.: 1139.  (3.21 MB)
Kleckner A, Sutton R, Yee D, Wong A, Davis J, Salop P. 2023 RMP Sediment Cruise Sampling and Analysis Plan. Richmond, CA: San Francisco Estuary Institute; 2023 . Report No.: 1138.  (445.99 KB)
Davis J. 2023 RMP Update. Richmond, CA: San Francisco Estuary Institute; 2023 . Report No.: 1148.  (37.75 MB)

Where Our Clean Water Program Works