Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, 15which will escalate the amount of terrestrial runoff entering coastal ecosystems. Prokaryotes are known to respond quickly to environmental change, making them potentially valuable earlywarning bioindicators, but relatively little is known about their short-term responses during extreme storms in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess prokaryotic community dynamics and changes in 20 physicochemical properties during early-and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment-locally known as red soil pollution-and caused moderate increases of macronutrients-especially SiO2 and PO4. Rather than shifts in marine bacteria, we primarily detected influxes of common soil-derived bacteria, and putative coral and human pathogens that may derive from other 25 sources; mesocosm experiments confirmed that soil input did not differentially affect marine bacteria. The storm effects on bacterial communities were short-lived and baseline assemblages were quickly recovered following disturbances. Early-and late-season storms caused different physicochemical and bacterial community changes. Our results demonstrate rapid and context-dependent shifts in prokaryotic communities due to extreme storm events in a 30 subtropical coastal ecosystem.