Hydrologic disturbances can alter algal communities, yet how these communities will respond to predicted increases in runoff associated with extreme precipitation events with climate change remains poorly understood. Precipitation has increased globally and is expected to continue changing in both frequency and intensity. Extreme precipitation events and associated flood pulses influence nutrient loading and water-column mixing in lakes which are key regulators of plankton succession, particularly in subtropical systems. However, it remains unclear how biological communities respond to these pulses and whether their responses are transient or persist over longer timescales. Understanding how hydrologic disturbance affects the temporal dynamics of algal communities is critical for predicting future lake conditions. We used three years of bimonthly data on benthic diatom composition from 14 sites across canal and pelagic zones to examine how a flow pulse associated with Hurricane Ian influenced benthic diatom assemblages in Lake Okeechobee, Florida. We assessed temporal changes in diatom communities in both zones in relation to flow, hypothesizing that assemblages would exhibit season patterns in species composition punctuated by flow pulse disturbances. Over the three-year period, diatom assemblages displayed clear seasonal cycles, with winter and summer communities differing consistently. Additionally, assemblage composition shifted over time after a large initial flood pulse of 40 m3/s that declined to a minimum of 4 m3/s. Flow emerged as a key driver of benthic diatom community structure in Lake Okeechobee, with observed compositional shifts likely reflecting lagged effects of Hurricane Ian that persist three years later. This research provides insight into algal community resilience and recovery following extreme precipitation and resultant flood pulse disturbances, which is essential for interpreting algal responses to other stressors, including nutrient enrichment, and for understanding implications for harmful algal bloom formation.