San Francisco Estuary and Watershed Science

Cyanobacteria harmful algal bloom (CHAB) events, often dominated by the cyanobacteria genus Microcystis, are a major water-quality issue in the large, hydrologically complex, Sacramento–San Joaquin Delta (Delta). To improve future CHAB-specific monitoring, we analyzed historical data to characterize spatial and habitat-based patterns in CHAB occurrence. We identified three primary habitat types that support CHABs to various degrees: (1) dead-end channels and marinas, which tend to support the highest densities and most frequent blooms; (2) flooded islands, shallow side channels, and sloughs, where CHABs occur less frequently, and generally at lower densities, and (3) main channels, where CHABs occur but typically at lower intensities and without the surface accumulations observed in dead-end channels. Data from routine monitoring programs and special studies were used to evaluate CHAB variation across Delta regions and among these habitat types. Monitoring metrics included chlorophyll-a (chl-a), Microcystis abundance determined by microscopy and quantitative polymerase chain reaction (qPCR), microcystin toxin concentrations, and Microcystis Visual Index (MVI) scores. July through October was identified as peak CHAB season, with CHAB severity greatest in the South Delta, Central Delta, and San Joaquin River regions. CHABs and associated toxins were infrequent in the Sacramento River, Cache Slough Complex, and East Delta regions, with microcystin concentrations typically below detection (0.15 µg L–1) and always below the California health-based warning trigger of 6.0 µg L–1. Dead-end channel habitats exhibited significantly higher microcystin concentrations than other habitat types, with nearly 40% of samples exceeding the California caution trigger of 0.8 µg L–1, compared to 10% in flooded islands and 7% in main channels. Based on these findings, we recommend enhanced sampling in dead-end channels and continued CHAB monitoring to identify and refine risk forecasts under changing climate conditions.