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by Spencer Fern, Delta Science Coordinator, Restore the Delta

Harmful algal blooms (HABs) are a nuisance species of algae that form in conditions of high nutrient loads (Nitrogen and Phosphorous), stagnant waters (low-flow conditions), sunlight exposure, water clarity, high water temperatures (generally > 75° F), as well as salinity (however HABs are becoming increasingly salt tolerant).

In the San Francisco Bay-Delta the species of HABs we know to be the most harmful are:

  • Microcystis
    • Active toxin: microcystins
  • Anabaena AKA Dolichospermum 
    • Active toxin: anatoxins
  •  Aphanizomenon
    • Possible active toxins: microcystins, anatoxins, cytotoxins

These are specifically freshwater HABs (FHABs) which thrive off the stagnant fresh water in the dead-end sloughs around the Delta in areas like Stockton, Discovery Bay, Antioch, Rio Vista, and Franks Tract. This proliferation raises concerns about health of the ecosystem as well as those living near the water. 

Who and what is affected?

  • Unhoused population living near Mormon Slough, residents recreating and living near the waterfront in downtown Stockton, residents living adjacent to waterways in Discovery Bay, and residents recreating near Big Break in Antioch.
    • Transmission from HABs infested water can be caused by ingestion (possibly leading to liver issues or death), skin contact (causing rashes), or even possibly inhaling aerosolized toxins (still being studied by UNC).
    • A local pediatrician with a practice in Discovery Bay is tracking a series of illnesses in children and exploring links to cyanotoxin exposure.
  • Fish populations can be killed off because when HABs start to die off, they take up the majority of dissolved oxygen (DO) in the water, which essentially suffocates fish. This past year, San Francisco experienced a HAB outbreak that experienced fish kills in response to lack of dissolved oxygen.
  • Ecological conditions worsen, plants and fauna must fight for light availability because blooms can block sunlight from penetrating the water column.

What Did We See in Stockton in 2022?

           Last year we sampled seven sites around Stockton and we tested using Microcystin Test Strips to grab base values for possible toxin levels. The sites worth mentioning:

  • Mcleod Lake, specifically off the catwalk in downtown Stockton, had the most and longest stretch of bloom activity, breaking the limit of our test strips from July to the end of August.
  • Mormon Slough, which is close to Mcleod Lake, but didn’t show as high of bloom activity, but worth noting because of the unhoused encampments on Mormon Slough.
  • Smith Canal, more specifically American Legion Park, which was the first bloom we saw last year, had high levels of toxins for a stretch that raised concerns because people fish here, have picnics, and live there in the houses around the park.

The test strips allowed us to collect base readings, but we sent off samples to UC Santa Cruz to run more specific DNA tests on the exact types of toxins and to help confirm what we were seeing in the field, and we were able to confirm our readings in Mormon Slough and Mcleod Lake. In the samples sent to UCSC we were able to confirm the types of toxins, including the specific strands of Microcystis and other toxins that may be present. According to the samples sent, we never saw any indication of other toxins aside from microcystins in Stockton.

CA Water Agency News from the Past Two Years:


           Keith Bouma-Gregson, and other staff of USGS, made a proposal in November of 2021 to secure funding to add cyanotoxin monitors to existing monitoring stations around the Delta to be able to collect continuous toxin data from the Delta waters. The problem is that they already had 6 stations in place at the time of writing this proposal, but funding was running out and would shut down those cyanotoxin monitoring stations, with some contracts ending in 2022. USGS staff also mention wanting to use SPATT (solid phase adsorption toxin tracking), which collects toxin data in the water over a period of time (instead of once at one time, like the test strips). Effective to use in conjunction with other means of testing.[1]

FHAB Program (DWR, CADFW, State Water Board):

           In a legislative report in 2022 for the FHAB Program, the issue of HABs impacting reservoirs on the State Water Project was raised as a concern. It was also mentioned that there was a standard for HABs in drinking water, and while acknowledging beneficial uses, they left out creating a standard for recreational uses. The members of the FHAB program recognize HABs as a dynamic threat and that we don’t know enough about HABs to make thorough decisions. The challenge is funding and how being able to monitor HABs requires a lot of volunteering from local water groups around the Delta. They want to form a standard for water quality objectives so that HABs measures can be enforced.[2]


           Haley Plaas and Hans Paerl are still analyzing data they collected from monitoring sites in Stockton and Discovery Bay to find a link between HABs and Air Quality. Their strategy is to look at PM 2.5 and PM 10 readings for aerosolized toxins, and this coming year they will be adding Antioch as a testing site. When we know more, we can start to advocate for more.

[1] Bouma-Gregson K, Hansen A, & Kraus T. 2021. Cyanotoxin Monitoring in the Delta: Leveraging existing USGS and DWR field efforts to identify cyanotoxin occurrence, duration, and drivers Problem Statement. [accessed 2023 Feb 23]. https://deltarmp.org/Documents/FY2021_DRMP_HABs_Proposal.pdf.

[2] Legislative Mandated Report: 2022 Water Code Section 13182(a) Comprehensive Report. [accessed 2023 Feb 23]. https://www.waterboards.ca.gov/water_issues/programs/swamp/docs/2022/2022-legislative-mandated-report-final.pdf.