To investigate the response of a subtropical coastal phytoplankton community to tropical cyclones, we utilized high temporal resolution (hours) data from the Imaging FlowCytobot (IFCB) deployed in the Gulf of Mexico. In 2010, four tropical cyclones (two during June–July and two during September) struck the area. Passage of the cyclones produced two major impacts: (1) storm surges and strong onshore winds, and (2) heavy rains producing substantial freshwater discharge and decreased salinity. The phytoplankton community showed a rapid response to the passage of the cyclones with increased abundance. Using principal component analysis, responses during storm surges and after freshwater discharges were distinguished and considerable changes in community composition were revealed. Responses to storm surges were characterized by an increase of diatoms. Freshwater discharges triggered increases in dinoflagellates and other flagellates (prasinophytes, euglenophytes, and cryptophytes) relative to the other groups. In June–July, substantial increases in diatoms were also observed. The response to freshwater discharge during this period was dominated by a diatom (Thalassiosira), whereas in September the response was dominated by two dinoflagellates (Akashiwo sanguinea and Polykrikos hartmannii). Observed abundances of these three taxa were the highest recorded from the IFCB time series. The short-term responses of the phytoplankton community revealed here emphasize the need for high temporal resolution sampling to fully capture the effects of tropical cyclones. Given that extreme storms are predicted to increase with future climate change, the taxonomic resolution of the IFCB is also valuable for detecting taxa-specific responses, which can have implications for ecosystem functioning.