Home > Explore Projects > Advancing an Integrated HAB Detection and Monitoring System Across the San Francisco Estuary
NCCOS Project

Advancing an Integrated HAB Detection and Monitoring System Across the San Francisco Estuary

This project began in September 2023 and is projected to be completed in August 2028.

This project will improve monitoring and response to harmful blooms of cyanobacteria and marine algae and a suite of algal toxins they produce that have been documented across the freshwater to marine continuum throughout the San Francisco estuary. The effort will provide the technical foundation, program design, and strategic plan for an estuary-wide harmful algal bloom (HAB) monitoring program. Key stakeholders will be engaged to help identify support needed to sustain the program.

Why We Care
Over the last decade, harmful algal blooms (HABs) have emerged as one of the highest-priority water quality management issues in the San Francisco estuary — the U.S. Pacific Coast’s largest estuarine system, which includes San Francisco Bay and the Sacramento-San Joaquin Delta. Although the bay has been recognized as nutrient-enriched for decades, there has not been a severe HAB event until recently. However, recent studies have determined that multiple HAB-forming organisms and HAB toxins are commonly detected in the bay, highlighting the risk for a major HAB event. In 2022, an unprecedented Heterosigma akashiwo bloom caused the first HAB-related fish kill and low dissolved oxygen event in the bay since water quality monitoring began in 1969. Further, in the delta, cyanobacterial blooms and associated toxins have expanded in frequency and severity since they were first recorded in 1999.

Scientists, regulators, managers, and stakeholders have spearheaded major expansions in HAB monitoring over the last decade, leading to improved understanding of both HAB-related conditions and data types needed to effectively monitor HABs. However, these activities largely proceeded as separate, subregional, and limited-duration research projects. The estuary’s large spatial footprint spans multiple regulatory jurisdictions and management agencies that have different regulatory mandates and management drivers, with limited impetus or opportunity for interagency engagement on HAB monitoring. As a result, there is currently no sustained, coordinated program for monitoring HABs across the freshwater to marine continuum in the estuary.

What We Are Doing
The project team will establish the technical foundation, program design, and strategic plan for developing and implementing a cost-effective, system-wide HAB monitoring program for the San Francisco estuary.

The team will accomplish this goal by pursuing four objectives. The team will enhance existing monitoring data sources with new technologies and tools – DNA-based techniques for quantifying HAB species (qPCR, metabarcoding), remote sensing, and leveraging community science for expanded monitoring coverage – to facilitate the rapid detection of HAB events and to further our understanding of HAB drivers and ecology. All data streams will be integrated into an estuary-wide HAB dashboard, to deliver data rapidly to managers and serve as a decision support tool to inform HAB-related management. The team will fill data and knowledge gaps about cell and toxin transport along the freshwater to marine continuum. The team will also develop a coordinated HAB monitoring and management strategy across the estuary to improve HAB event response and manage HAB impacts.

The project leverages a multi-decade USGS water quality monitoring program and investments in HAB monitoring pursued through the Bay Nutrient Management Strategy.

This project is led by co-principal investigators Dr. David Senn, San Francisco Estuary Institute, Dr. Keith Bouma-Gregson, USGS California Water Science Center, and Dr. Ellen Preece, California Department of Water Resources. Co-investigators are: Dr. Ariella Chelsky, San Francisco Estuary Institute, Dr. Raphael Kudela, University of California Santa Cruz, Dr. Meredith Howard, Central Valley Regional Water Quality Control Board, Dr. Thomas Mumley, San Francisco Regional Water Quality Control Board, Dr. Timothy Otten, Bend Genetics, LLC, and collaborating NCCOS scientists are Dr. Richard Stumpf, Dr. Michelle Tomlinson, and Jennifer Maucher Fuquay. The project team directly engages managers and other stakeholder scientists to ensure results will support priority management needs and contribute to a more effective and efficient HAB strategy in the estuary.

The team will also meet regularly with a management transition advisory group (MaTAG) to facilitate the transition of piloted detection methods and monitoring strategies to enhance federal state and local programs. The MaTAG includes the San Francisco Regional Water Quality Control Board, Bay Area Clean Water Agencies, San Francisco Baykeeper, California State Water Resources Control Board, California Department of Fish and Wildlife, NOAA Fisheries California Coastal Office, Central Valley Regional Water Quality Control Board, California Department of Water Resources, Delta Stewardship Council, and Restore the Delta.

This project is supported by the NCCOS Monitoring and Event Response for Harmful Algal Blooms (MERHAB) Research Program.

Benefits of Our Work
This project will lead to demonstrable changes in knowledge broadly benefiting the estuary management community, including refined and expanded use of qPCR and metabarcoding to improve algal species detection specificity, limits, and sampling time and yield a better understanding of HAB dynamics. In the region, it will clarify whether HAB taxa and toxins move between the delta and bay and improve satellite remote sensing output for smaller waterways to inform timely responses. These enhancements can inform the design of monitoring programs and support future policy amendments or changes to better manage nutrients and address HAB-related water quality impairments, and reduce the potential for future HAB events in the San Francisco estuary.

Additional Resources

Click to expand resource list(s).

Explore Similar Projects
No posts found.


NCCOS delivers ecosystem science solutions for stewardship of the nation’s ocean and coastal resources to sustain thriving coastal communities and economies.

Stay Connected

Sign up for our quarterly newsletter or view our archives.

NCCOS Multimedia

Visit our new NCCOS Multimedia Gallery. 

Follow us on Social

Listen to our Podcast

Check out our new podcast "Coastal Conversations"