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In arid and semi-arid regions, a hydrological regime characterized by an annual cycle of drought and rainy seasons changes the volume and retention time of reservoirs. Such changes affect the limnological characteristics and lead to changes on phytoplankton community. Phytoplankton seasonal succession was studied in a Brazilian eutrophic semi-arid water supply reservoir (Cruzeta). In this study, the changes in the biomass and species composition of phytoplankton during two annual hydrological cycles were analyzed, and the driving factors were evaluated. The composition of phytoplankton alternated between filamentous cyanobacteria, such as Cylindrospermopsis raciborskii, under conditions of mixing, and colonial species, such as Microcystis panniformis and Sphaerocavum brasiliensis, under conditions of high water column stability. The lower water level during a severe drought favored adaptive phytoplankton species with low requirement for resources, such as diatoms and cryptomonads. Extreme events, i.e., torrential rains and severe droughts, governed by the hydrological regime of the semi-arid region led to strong altered availability of resources in the watershed, directing the spatial and temporal dynamics of the phytoplankton in the Cruzeta man-made lake. The results showed an unusual behavior of the phytoplankton community contradicting the expectations about the climatic change scenario. Instead of an expected increase in cyanobacteria, the severe drought led to low biomass and resources, favoring diatoms and cryptomonads.