SCIENCE SPOTLIGHT: Managing a Cyanobacteria Harmful Algae Bloom “hotspot” in the Upper San Francisco Estuary

At the January meeting of the Delta Stewardship Council, interim Delta Lead Scientist Dr. Lisamarie Windham-Myers highlighted recent research on Harmful Algal Blooms, and highlighted upcoming Delta science events.

This month’s article spotlight focuses on research funded by the Delta Science Program on the harmful algal blooms in 2022, a uniquely bad year for the toxic menace.  The research, led by Ellen Preece, focused on how nutrient loading affected cyanobacteria harmful algae blooms (CHABs) in the Deep Water Ship Channel and the Stockton waterfront area in the summer of 2022 and considered four categories of management actions to mitigate the occurrence and impact of the blooms.

There are many different kinds of algae blooms, and they are becoming increasingly persistent within the San Francisco Estuary due to increased water temperatures, extreme climate events, and over-enrichment of nutrients in the water, which is usually thought of as the source of the problem.   Cyanobacteria harmful algal blooms (CHABs) are harmful to ecosystems and can result in large fish kills when they occur.  Large estuarine systems, such as the San Francisco Estuary, can be prone to hotspots for various reasons,  such as sources of nutrients, freshwater stagnation, or pulses related to storm events.

The study focused specifically on the Deep Water Ship Channel and the Stockton waterfront, where a CHAB event occurred during the summer of 2022.  The study considered potential causes, such as nutrient loading in the surface water and nutrients potentially in the sediments.

Within this area, the study looked at nitrogen and phosphorus concentrations in the surface water and whether the algal bloom distribution in this region was responding to these as growth-limiting nutrients.  They also tested whether phosphorus in the sediment, especially the water within the sediment (pore waters), could help predict HAB distributions.  These measurements during the large HAB event of 2022 were characterized in time and space to identify potential management actions that could be implemented to reduce HAB intensity and/or frequency in a tidally influenced estuary.

The researchers characterized the time and space from McCloud Lake to the confluence with the San Joaquin.  While other species were present, the microcystis shown on the boat ramp in the picture is blue-green algae, which was found to be the most abundant algal species.  They found that nutrient concentrations in the Stockton channel were particularly high, even for this region, which is normally high.

The researchers determined the blooms were tied to several factors, with no clear culprit they could point to.  There was a large nutrient pool in not just the water but also the sediments below, and high concentrations of microcystis at all eight sites in the study, but especially at Waterfront 3 had the highest density and the most severe bloom.

“The high concentrations of overall chlorophyll, they’re not totally abnormal, but they’re in the higher 99 percentiles of what we find in the Bay and Delta,” said Dr. Windham-Myers (CHECK).

Waterfront 3 was consistently the shallowest and warmest site, and microcystis grows well under those warm conditions.  The bloom led not only to toxin production but also likely a high pH and raised oxygen levels, which can create a positive feedback loop by which the cysts of the algae can persist in the sediments.   All of these events occurring together created the ideal environment for this particular bloom to persist, which it did until December 2022.

To reduce the intensity and frequency of CHABs in the future, the paper outlined four main categories and management tools to mitigate against CHABs and whether they would likely make a difference in the Stockton channel:

  1. External nutrient control
  2. Chemical controls, such as algaecides or barley straw – anything that can be put in there to absorb the available nutrients to outcompete the cyanobacteria.
  3. Aquatic vegetation as a biological control because it could compete for those nutrients and hold back the cyanobacteria growth.
  4. Physical or mechanical controls by using flows to disrupt the lifecycle of the cyanobacteria and prevent the accumulation of colonies or dredging below that can remove the seed stock of the cyanobacteria in the soil.

“For example, even though reducing the nutrients added to the system would be ideal in the long term, it’s not clear that that’s going to solve the problem here because the nutrients were so high, and it wasn’t necessarily where the bloom was happening was where the nutrients were the highest,” said Dr. Windham-Myers. “So instead, they suggested increasing the recirculation of water in the short term, particularly at Waterfront 3, to help reduce a CHAB bloom in that area.”

“They also noted that there were oxygen diffusing bubblers along the waterfront that have been used to alleviate the low dissolved oxygen concentrations that persist in that area.  But they didn’t provide enough turbulence in the water to break up these kinds of scummy colonial algae to create the physical disruption that can help flush things out and prevent the long-term persistence of these blooms.”

The Delta Science Program hosted a HABs workshop in 2022 and has been facilitating the development of an interagency monitoring strategy since then.  The authorship team will release the draft HABs monitoring strategy for public comment this spring and host a Delta agency science workgroup to discuss shared community implementation of the strategy.

“So we are actively working on this issue because it’s probably not going away anytime soon,” concluded Dr. Windham-Myers.


The 12th Annual 2024 Bay-Delta Science Conference will be held at the SAFE Credit Union Convention Center in Sacramento from September 30 to October 2, 2024.  The Delta Stewardship Council’s Delta science program and USGS have co-sponsored this event every two years since 2000.  This year’s theme, ‘ Cultivating Connections in a Dynamically Changing Environment,’ recognizes the need for diverse perspectives to confront multiple challenges and a dynamically changing environment such as the Sacramento San Joaquin Delta.  The conference will include talks and sessions encompassing a wide variety of disciplines, such as using traditional knowledges, identifying contaminants within and around the watershed, identifying the needs of various species, and exploring ways to mitigate climate change impacts, among other topics.  Registration and a call for session abstracts will open later this spring.

The Executive Summary was recently released for the 2022 edition of the State of Bay-Delta Science, which included seven peer-reviewed articles exploring the latest scientific understanding of the ecosystem roles of plants and algae in the Bay-Delta.  The complete edition emphasizes the benefits and the negative impact of different species of plants and algae on the region’s ecosystems and human uses.  This executive summary offers a condensed version of the overall edition of SBDS.  It provides a snapshot of the main topics covered in each article, highlighting key takeaways and summarizing the next steps to consider for future science and management actions.  The issues explored in the SBDS edition include ecosystem services and disservices of plants and algae, primary production, ecology of aquatic vegetation, aquatic vegetation control, remote sensing methods, harmful algal blooms, and carbon sequestration and subsidence reversal.

The State of the Estuary Conference is scheduled for later this spring at the Henry J. Kaiser Center for the Arts in Oakland.  The San Francisco Estuary Partnership organizes this event every two years to highlight the current management and ecological health of the San Francisco Bay-Delta Estuary.  The conference provides a critical venue for drawing deeper connections across individuals and institutions working on climate adaptation, environmental justice, and regionwide watershed stewardship.  Attendees include regional scientists, community organizers, students, legislators, resource managers, planners, and others working on issues related to improving, conserving, and monitoring the health of the estuary.  Organized sessions and posters will focus on living resources, water quality, climate resilience, and environmental stewardship.  Additional pre-conference workshops will take place on March 11.

The Salinity Management Workshop will be held on March 26 and 27.  The Delta Science Program is hosting this two-day online workshop to discuss tools and strategies, identify knowledge gaps, and build shared goals for adaptively managing ocean saltwater intrusion in the Delta.  Presentations will include the human dimensions of salinity management and modeling tools to assess the impacts of various management actions.  There will be interactive sessions to share ideas and gather input from participants about the impacts of management actions, their trade-offs, and ways to improve modeling tools.  The full agenda will be released later this month.

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