The St. Lucie Estuary, located on the southeast coast of Florida, provides an example of a subtropical ecosystem where seasonal changes in temperature are modest, but summer storms alter rainfall regimes and external inputs to the estuary from the watershed and Atlantic Ocean. The focus of this study was the response of the phytoplankton community to spatial and temporal shifts in salinity, nutrient concentration, watershed discharges, and water residence times, within the context of temporal patterns in rainfall. From a temporal perspective, both drought and flood conditions negatively impacted phytoplankton biomass potential. Prolonged drought periods were associated with reduced nutrient loads and phytoplankton inputs from the watershed and increased influence of water exchange with the Atlantic Ocean, all of which restrict biomass potential. Conversely, under flood conditions, nutrient loads were elevated, but high freshwater flushing rates in the estuary diminished water residence times and increase salinity variation, thereby restricting the buildup of phytoplankton biomass. An exception to the latter pattern was a large incursion of a cyanobacteria bloom from Lake Okeechobee via the St. Lucie Canal observed in the summer of 2005. From a spatial perspective, regional differences in water residence times, sources of watershed inputs, and the proximity to the Atlantic Ocean influenced the composition and biomass of the phytoplankton community. Long water residence times in the North Fork region of the St. Lucie Estuary provided an environment conducive to the development of blooms of autochthonous origin. Conversely, shorter residence times in the mid-estuary limit autochthonous increases in biomass, but allochthonous sources of biomass can result in bloom concentrations of phytoplankton.