Exploring factors that affect Microcystis abundance in the sacramento san joaquin delta

•Management tools are needed for Microcystis in the Sacramento San Joaquin Delta.•Low salinity zone not a good proxy for residence time where Microcystis most severe.•Climatic conditions have the greatest influence on Microcystis biovolume in the Delta.•Flow and temperature do not explain interannual Microcystis biovolume differences.•Increasing flow may be ineffective at reducing Microcystis if temperatures are high. Cyanobacteria harmful algal blooms (cHABs) are increasing in frequency, intensity and duration in estuaries worldwide. In the upper San Francisco Estuary, also known as the Sacramento San Joaquin Delta (Delta), cHABs have been a topic of concern over the past two decades. In response, managers are urgently working to understand the factors that drive cHABs and identify feasible management options to avert ecological and human health consequences. We used a six year data set to explore relationships between flow parameters, temperature, and Microcystis biovolume to determine the potential for managing large scale hydrodynamic conditions to address Delta cHABs. We also looked at the relationship between Microcystis biovolume and the low salinity zone to see if it could be used as a proxy for residence time, because residence time is positively related to cyanobacteria abundance. We found the low salinity zone is not a useful proxy for residence time in the area of the Delta that experiences the most severe cHABs. Our finding suggest that climatic conditions (i.e., temperature and water year type) have the greatest influence on Microcystis biovolume in the Delta, with higher biovolume during years with lower flow and higher temperatures. Further, there are interannual differences in Microcystis biovolume that cannot be fully explained by flow parameters or temperature, meaning other factors not included in our model may be involved. We conclude that management actions to increase flow may be ineffective at reducing Microcystis to desired levels if water temperatures remain high.