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Extreme events can cause species substitution or biodiversity losses. In floodplains, flood and drought phases are considered disturbances when their amplitude or intensity are atypical. These unpredictable events can affect the structure of aquatic communities. In this context, we evaluated the response of the zooplankton community to two extreme droughts that occurred from 2001−2002 and 2014−2016. We assessed species richness and composition on three occasions: before extreme drought (phase 1); during the phase after extreme drought (phase 2) characterized by floods, and lastly, after flood (phase 3), when the fluctuations in water levels in the lowlands stabilized. We hypothesized that (i) zooplankton composition in the lake is distinct in the phases before extreme drought and flood, as the extreme drought event causes changes in the community structure and (ii) after the flood (phase 3), the composition of species in the lake would be more similar to the phase 1, with a large number of species shared in these. Contrary to what we expected, similarity in the species composition of the lake was greater between the phase 1 and phase 2, which may indicate the resilience capacity of the community, through specialized adaptations capable of tolerating extreme. The lowest similarity was observed between the phase 1 and phase 3 and this difference may be a consequence of the dilution effect of the community in the flood (phase 2). Our results suggest that the community structure in the lake can be considered more resilient to extreme drought. We also highlight the importance of the hydrological dynamics of a floodplain for the structure of communities, considering atypical droughts in periods of different climatic events.