Water Quality Monitoring

Many of the Water Boards' water quality protection programs rely on monitoring data, which we and other agencies collect for our own use and also make available to the public. This page details many of our water quality monitoring efforts and includes links to water quality information in our area.

SWAMP / North Bay Fires / CyanoHABs / RMP / BASMAA Monitoring / Special Studies / Past Programs / Groundwater / Contact

Water quality monitoring is important for many reasons. Monitoring results allow the Water Board to set program priorities and budgets as well as report our successes and challenges to our sister agencies at the regional, state, and federal levels. The Bay Area is fortunate to have monitoring partners who are committed to excellence in this ongoing work.

Surface Water Ambient Monitoring Program (SWAMP)

Statewide SWAMP monitors water quality in wadeable streams and conducts screening studies to measure levels of pollutants in fish from waterbodies where people fish and consume their catch. The goals of past surface water monitoring programs -- Mussel Watch, Toxic Substance Monitoring, Coastal Fish Contamination, and Toxicity Testing programs -- are now included under SWAMP. The Surface Water Ambient Monitoring Program, or SWAMP, is designed to assess the conditions of surface waters throughout California. There are statewide and regional components to SWAMP.

Statewide SWAMP
High-quality data is a statewide priority for SWAMP. The SWAMP Quality Assurance Program Plan (QAPrP) is now the statewide standard for surface water monitoring conducted under all State Water Board programs and grants. The plan was updated in 2008.

SWAMP is making data available to the public via the California Environmental Data Exchange Network (CEDEN). In addition, through the California Water Quality Monitoring Council’s website information is available to answer basic water quality questions such as: 1) is the water safe for swimming? 2) is the water safe for drinking? 3) Are fish and shellfish safe to consume? and 4) is aquatic life protected? This information is available statewide and for individual waterbodies.

Statewide Freshwater CyanoHABs Strategy - SWAMP has developed an assessment and support strategy for statewide coordination to address freshwater harmful algal blooms (HABs). This strategy outlines a number of projects that SWAMP is funding to assist with the assessment of HABs throughout the state, and support water managers dealing with HAB issues. More information is being provided through the website for the California CyanoHAB network.

For more information about SWAMP Statewide and to obtain documents and reports go to http://www.waterboards.ca.gov/water_issues/programs/swamp/

Bay Area SWAMP
The mission of SWAMP is to monitor the ambient condition of waters throughout the State. SWAMP also develops assessment methods (e.g., standard operating procedures and interpretative tools) and quality assurance guidance for water quality monitoring. SWAMP supports monitoring coordination among Regional Water Boards, permittees, and statewide monitoring programs.

In particular, the Bay Area SWAMP program supports regional coordination of water quality monitoring among permittees, public agencies, and citizen monitoring groups by providing training for SWAMP sampling methods, data entry using SWAMP templates, and data upload to the California Environmental Data Exchange Network (CEDEN). Since 2000, SWAMP has collected stream water quality data (e.g., metals, nutrients, pathogen, toxicity, bioassessment) from over 200 locations throughout the Bay Area. These SWAMP data have supported many Regional and State Board activities including: providing a large proportion of data used to write the Integrated Report for 303d listing and 305b assessments, determining regional reference conditions, supporting TMDL developments, and providing background information for 401 certifications, NPDES permits, and conditional waivers of waste discharge requirements.

Bay area SWAMP has also examined contaminants in fish from 27 lakes at an intensity necessary for the Office of Environmental Health Hazard Assessment (OEHHA) to develop fish consumption advisories. In Suisun Bay, studies of nutrients and their effect on phytoplankton growth have been conducted to support nutrient objective development, modeling and NPDES permitting. These studies have been conducted in collaboration with the State and Federal Water Contractors Agency (SFWCA), Central Contra Costa Sanitation District (CCCSD) and Bay Area Clean Water Agencies Association (BACWAA).

In 2010, SWAMP started working with SFSU Romberg Tiburon Center to measure nutrients and chlorophyll a in Suisun Bay in the spring in order to determine causes of the decline in spring diatom blooms. In 2011-12 the study will be conducted as a collaboration between SWAMP, the state and federal water contractors, Bay Area Clean Water Agencies (BACWA) and Central Contra Costa Sanitary District. Through the collaboration, primary production, nutrient uptake and pesticides will be monitored in addition to nutrients and chorophyll a. Toxicity Identification Evaluations (TIEs) will also be conducted to determine the cause(s) of toxicity.

Currently, one of the major roles of the Bay Area SWAMP is to participate in a watershed monitoring coalition (BASMAA Regional Monitoring Coalition) with stormwater programs to ensure collaborative, consistent, and high-quality watershed monitoring. Since 2012, SWAMP has collected data from 20 non-urban streams throughout the Bay Area to put this urban monitoring into context.

In the San Francisco Bay Area, our regional SWAMP has conducted monitoring that has resulted in 3 types of reports:

  1. SWAMP has measured contaminants in fish from ten reservoirs, Tomales Bay, and other coastal areas. These studies have led to fish consumption advisories developed by the Office of Environmental Health Hazard Assessment (OEHHA) available at http://www.oehha.ca.gov/fish.html
  2. SWAMP has developed a rapid trash assessment protocol that has been used to measure trash in 14 watersheds. Studies took place after wet and dry seasons to determine sources of trash as well as accumulation levels. Rapid Trash Assessment Report (pdf, 1.2MB) This information was used to place many Bay area creeks on the 303(d) impaired waterbodies list. Since then, the Municipal Regional (stormwater) Permit (MRP) was approved that requires municipal stormwater programs to control trash in various ways.
  3. Over 5 years SWAMP used bioassessments, water and sediment chemistry and toxicity tests, as well as continuous monitoring probes for temperature, dissolved oxygen, pH, specific conductance, and depth to measure water quality in 34 watersheds and sub-watersheds throughout the region. Reports are available interpreting the results. Please note that these are large files that may take a few moments to download.
From 2007 to 2010 the Bay area SWAMP monitored reference sites in the Bay area to provide perspective on previous monitoring and to assist efforts to develop bio-objectives and nutrient criteria. This report describes algae, benthic macroinvertebrate, nutrient, and physical habitat conditions in 3 perennial and 3 non-perennial reference streams.

San Francisco Bay regional SWAMP workplans

North Bay Fires in 2017

In October 2017, three large wildfires burned over 100,000 acres in the North Bay. Fires can cause significant increases in contaminants including nutrients (e.g. nitrates and phosphorus), polycyclic aromatic hydrocarbons (PAHs), copper, zinc, mercury, lead, and other metals, so we monitored for those pollutants in Napa River and Sonoma Creek watersheds. Results indicate water quality was not impacted by fires in either watershed. For more information please see the documents below. 

Cyanobacteria Harmful Algal Blooms (CyanoHABs)

Breaking - HAB Event of Summer 2022

During the summer of 2022, San Francisco Bay is experiencing a large bloom of the species, Heterosigma akashiwo, one of several species that can cause water to take on a reddish-brown color, commonly called “red tide”. Fish kills associated with this bloom have been occurring in several parts of San Francisco Bay and Lake Merritt. The Water Board is working through the Nutrient Management Strategy team to track observations of algae or wildlife impacts to understand the scope of the bloom. For more information, see these answers to frequently asked questions about this HAB event. This fact sheet explains how the Water Boards use satellite imagery to track red tide conditions as they develop.

Cyanobacteria, commonly known as blue green algae, are natural components of healthy marine and fresh water ecosystems. Under certain water quality conditions cyanobacteria can rapidly multiply causing nuisance "blooms." A small number of cyanobacteria species are capable of producing toxins that can be harmful to animals and humans.

Cyanobacteria harmful algal blooms (cyanoHABs), which contain these toxins, are of special concern because of their potential impacts on drinking water, recreation in lakes and rivers, and effects on fish and wildlife.

In recent years, there has been an increased frequency and severity of cyanoHABs around the world, including the San Francisco Bay Region.

The risk factors that contribute to freshwater cyanoHABs and nuisance blooms include nutrient (phosphorus and nitrogen) enriched waters, warming climate, and lower flows.  There is a current need to manage the risk from freshwater cyanoHAB blooms through improved monitoring, increased educational outreach, and remediation of toxic blooms. Regional Water Board staff is collaborating with local recreational agencies, lake and reservoir managers, county public and environmental health officials, and other federal, state, county, and non-governmental organizations to address these needs.

To Report a CyanoHAB Event
To notify the Water Boards and other agencies about freshwater cyanoHAB events in the San Francisco Bay Region follow these instructions:
  • Instructions
  • Reporting form under “Quick Links”, go to third column “Reporting Forms” and select from pull-down menu “Bloom” or “Human Illness” or “Animal Illness”, and click on “Go”

Websites with information on sampling and laboratory resources; algae identification; remediation; and other topics:

For additional information about the San Francisco Bay Region's cyanoHAB program please contact: May 2016 Public Workshop on Freshwater CyanoHABs

On May 9, 2016, San Francisco Bay Regional Water Board staff hosted a public workshop to discuss monitoring, assessment and response strategies for freshwater cyanoHABs, and provide information on the prevalence and effects of cyanoHABs. The agenda for the workshop and all presentations are available at the links below.

Regional Monitoring Program (RMP) for Water Quality in the San Francisco Estuary

The RMP is an innovative partnership between regulators, dischargers, industry representatives, community activists and scientists to measure water quality in the San Francisco Estuary. The program is designed around management questions important to the Regional Water Board for regulating water quality in the estuary. The San Francisco Estuary Institute manages the program and conducts many of the studies. The RMP includes a status and trends component that measures water and sediment chemistry and toxicity, contaminant levels in fish and bird eggs, and loading of chemicals of concern to the estuary. There are also pilot and special studies that address sources and loadings, fate and transport and effects of pollutants. For more information, click here.

BASMAA Regional Monitoring Coalition

Under the Bay Area Stormwater Management Agencies Association (BASMAA), the Phase I Municipal Stormwater permittees (Alameda, Contra Costa, San Mateo and Santa Clara Counties and the Cities of Fairfield, Suisun and Vallejo) work together as the Regional Monitoring Coalition to collect receiving water quality data. Types of data collected include bioassessment parameters, general water quality, toxicity, and concentrations of pollutants of concern, such as copper, mercury, PCBs, and others. All monitoring requirements are spelled out in Provision C.8 of the Municipal Regional Permit. Reports submitted by the Regional Monitoring Coalition are posted here.

Stormwater Monitoring Reports

PCB, Mercury, and other Pollutants of Concern Monitoring

Stormwater Monitoring Sampling Procedures and Quality Assurance Documents (2016-current)

Special Studies

Macroinvertebrates in Wildcat and San Leandro Creeks

Bar-built estuary studies in Marin County

Past Surface Water Monitoring Programs

State Mussel Watch Program (SMWP)
For 26 years (1977-2003) the SMWP collected transplanted and resident mussels and clams from the waters of California's bays, harbors and estuaries. Samples collected in the SMWP were analyzed for trace elements, pesticides, and PCBs. The SMWP provided the State Water Resources Control Board with a uniform statewide approach to the detection and evaluation of the occurrence of toxic substances in marine waters. The SMWP primarily targeted areas with known or suspected impaired water quality. Sampling stations were primarily selected by the six coastal Regional Water Boards. Information collected in the SMWP is still used by the State and Regional Water Boards, and other agencies to identify waters impacted by toxic pollutants.

Toxic Substance Monitoring Program (TSMP)
For 27 years (1976-2003) the TSMP collected fish and other aquatic life from fresh, estuarine, and marine waters. Samples collected in the TSMP were analyzed for trace elements, pesticides, and PCBs. The TSMP provided the State Water Board with a uniform statewide approach to the detection and evaluation of the occurrence of toxic substances. The TSMP primarily targeted water bodies with known or suspected impaired water quality. Most sampling stations were selected by the nine Regional Water Boards. TSMP data is still used by the state and regional boards and by other state agencies to identify waters impacted by toxic pollutants.

Toxicity Testing Program (TTP)
Resources from this program (1987-2002) were used to fund or supplement special studies designed to investigate waterways where toxicity water quality objectives were not being met, and tell us whether those surface waters could support biological communities in aquatic ecosystems. The program used reliable USEPA standardized toxicity testing procedures,  modified USEPA Toxicity Identification Evaluations, bioassessments, and supporting chemical analysis.

Coastal Fish Contamination Program (CFCP)
This program was initiated in 1998 to investigate the safety for humans to consume fish and shellfish caught in California's coastal waters. The Office of Environmental Health Hazard Assessment (OEHHA) assisted the Regional Water Boards in designing this program and evaluated the data to determine the need for fish consumption advisories.

Bay Protection and Toxic Cleanup Program (BPTCP)
The BPTCP began in 1990 and ended in 1999 The program was a comprehensive effort by the State Water Board and the Regional Water Quality Control Boards to programmatically link environmental monitoring and remediation planning. The BPTCP had four major goals:
  • Provide protection of present and future beneficial uses of bays and estuarine waters in California
  • Identify and characterize toxic hot spots
  • Plan for toxic hot spot cleanup or other remedial or mitigation actions
  • Develop prevention and control strategies for toxic pollutants

Statewide Groundwater Ambient Monitoring & Assessment Program (GAMA)

GAMA is a statewide program that monitors regionally and also undertakes special studies. The main objectives of the program  are to improve statewide ambient groundwater quality monitoring and assessment, and increase the availability of information about groundwater quality to the public. Participation in the GAMA Program is voluntary; stewardship of the state's groundwater resources is the shared responsibility of all levels of the government and community. GAMA has produced numerous reports and other products on groundwater quality investigations throughout California. They can be found here.

For more information about GAMA, contact Cheryl Prowell (Cheryl.Prowell@waterboards.ca.gov) (510) 622-2408.

For more information contact:

Kristina Yoshida
Regional Monitoring and Assessment Coordinator
Phone: (510) 622-2334
Email: Kristina.Yoshida@waterboards.ca.gov