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Abstract Arid subtropical climates often oscillate between drought and wet conditions, leading to a “flood or famine” paradigm for estuarine freshwater inflow, in which sporadic storm events drive dynamic changes in salinity and nutrient availability. Transitioning from prolonged drought to wet conditions can impact phytoplankton communities. The Mission‐Aransas Estuary, located on the south Texas coast, transitioned from a 5‐yr drought (2010–2015) to wet conditions (2015–2020), punctuated by several large flood events and the direct impact of category 4 Hurricane Harvey. Using an 8‐yr bimonthly sample set (2012–2019), we evaluated particulate organic carbon, chlorophyll a , nutrient concentrations, and accessory pigments to characterize the response of the phytoplankton community to these climate events. We found that phytoplankton biomass was diminished during severe drought and increased during prolonged wet conditions. The phytoplankton community switched from being diatom‐dominated during drought to cyanobacteria‐dominated following estuarine freshening, driven by lower salinity and increased nutrient availability. Seasonal fluctuations between taxa persisted regardless of climate condition. The drought‐to‐wet transition prompted a regime shift of the estuarine phytoplankton community to a new quasi‐steady state in the studied estuary. Globally, changing climate regimes may cause longer periods of extreme drought or wet conditions for estuarine systems. Detailed, long‐term ecosystem monitoring is necessary to fully evaluate ecological responses to extreme weather events, especially links between biogeochemical cycling and ecosystem function. These results suggest that oscillations between distinct wet and dry periods have lasting effects on primary productivity, phytoplankton community composition, and organic matter cycling in subtropical estuaries with long residence times.