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October 5, 2023

NOAA recently awarded a grant through its Monitoring and Event Response Research Program (MERHAB) to support the development of a harmful algal blooms (HABs) collaborative monitoring program for the San Francisco Estuary.

The monitoring program will be led by scientists at the San Francisco Estuary Institute, the U.S. Geological Survey California Water Science Center, and the California Department of Water Resources. It will leverage on-going research and monitoring activities in San Francisco Bay and the Sacramento-San Joaquin Delta (collectively referred to as “the San Francisco Estuary”) to build a robust system-wide HAB monitoring program for the San Francisco Estuary. The collaborative team includes the University of California, Santa Cruz, Bend Genetics, the San Francisco Bay and Central Valley Regional Water Quality Control Boards, San Francisco Baykeeper, Cal Maritime Academy, Restore the Delta, and NOAA-NCCOS.

The grant will enable the development of a sustained, Estuary-wide HAB monitoring program. Over the last decade, HABs have emerged as one of the highest-priority water-quality management issues in the San Francisco Estuary, which is the U.S. Pacific Coast’s largest estuarine system. The program will advance real-time monitoring, remote sensing, and use of molecular techniques to identify and predict the occurrence of HABs and the toxins they produce. These new approaches will provide information that can act as an “early warning” of HABs, assist water use operators in decision making, and build our knowledge of the cyanobacterial communities that cause HABs and the cyanotoxins produced.

Collection of six bay maps show colorful algae blooms developing expanding then returned to pre-bloom levels.
Remotely sensed chlorophyll estimates during the 2022 HAB event (mg m-3). Data are from the ESA Sentinel-3 satellite and are processed using a locally tuned algorithm for San Francisco Bay. Image courtesy of the San Francisco Estuary Institute.


Scientist on boat wearing blue pants, green shirt, hat, life jacket, holding white net, with bridge and land in background.
A USGS technician conducts a phytoplankton net tow to measure harmful algae and toxins in San Francisco Bay.

Program Objectives

  1. Enhance existing monitoring data tools to facilitate the rapid detection of HAB events and to further our understanding of HAB drivers and ecology.
  2. Building an online HAB dashboard to provide managers with a decision-support-tool for HAB mitigation.
  3. Improved understanding of HAB transport dynamics using multiple methods and molecular tools.
  4. Convening a Management Advisory Group composed of managers, regulators, and non-governmental organization (NGO) stakeholders to generate information necessary for developing a coordinated HAB strategy.

Looking Ahead

The collaboration will enhance and integrate HAB monitoring in the San Francisco Estuary - including leveraging the region’s long-term monitoring programs and other on-going nutrient and HAB monitoring. The project will further our understanding of HAB drivers and ecology. New information and understanding will support future decision-making related to nutrient management and HAB-related water-quality impacts and contribute to the long-term health of the San Francisco Estuary. 

A profile of a silver ship with a USGS logo, has three people standing at the bow end dressed in dark colors with yellow pers
The USGS R/V Peterson conducts monthly cruises covering the San Francisco Estuary up to the Sacramento River at Rio Vista, California. The USGS has been researching and monitoring the San Francisco Estuary since 1969. The R/V Peterson is a fundamental resource for water-quality monitoring in San Francisco Estuary and will be used in the MERHAB project.

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