Abstract
In the San Francisco Estuary (SFE), abundance of phytoplankton species and nutrient concentrationsand forms vary over short temporal and spatial scales. This makes it difficult to make conclusive statements about ecosystem responses to nutrient changes. Here we discuss results from using a commercially available instrument designed to continuouslyquantifymajor algal taxa in situ, based on fluorometric quantification of primary and accessory pigments. We also show how data from highfrequency (15 min) monitoring of algal pigments, nutrients (nitrate, ammonium and orthophosphate), and ancillary water qualityat a fixed station can provide insights into drivers of phytoplankton abundance and community structure. Finally, we demonstrate how high-speed (5 to >10 m s-1) boat mappingat high samplingfrequencies (1 cps) can provide additional insights into drivers of phytoplankton, help us resolve differences attributable to mixing of different water sources, and explore the complex linkages among time-dependent hydrologic and biogeochemical processes in the SFE.