San Francisco Estuary and Watershed Science

Cyanobacterial harmful algal blooms (CHABs), often comprising the cyanobacteria genus Microcystis, are an increasing water-quality concern in the large, hydrologically complex, Sacramento–San Joaquin Delta (Delta). Monitoring CHABs in estuarine environments is challenging because of the dynamic physical, chemical, and biological gradients across the freshwater–saltwater continuum. Here we provide an overview and synthesis of environmental drivers known to influence CHAB formation. We analyzed long-term environmental data— including flow, turbidity, temperature, salinity, and nutrients compiled from routine monitoring stations—to assess variability across seven defined regions of the Delta. Our results highlight significant differences in environmental conditions among regions. The upper San Joaquin River (USJR) region has previously been recognized as one of the areas in the Delta most prone to CHAB events, and in our analyses exhibited the highest summer water temperatures, elevated nutrient concentrations, and low turbidity all conditions that favor CHAB development. In contrast, the lower San Joaquin River (LSJR) and lower Sacramento River (LSR) regions had cooler temperatures and higher turbidity, which are generally less favorable for bloom formation. While water temperatures in the East Delta (ED) were relatively cool, they increased more rapidly than in other regions, with an observed warming trend in June of approximately 0.2 °C per year. The ED was also the region that had the least amount of environmental monitoring relative to the other study regions and had no consistent nutrient data. Enhanced monitoring in the ED and continued monitoring in the other regions will be critical for tracking climate-driven changes in environmental conditions that support CHAB proliferation.