Prolonged drought events are expected to become more frequent due to climate change. Although they already occur in semiarid regions, their impact on fish assemblages in reservoirs remains unknown. This study aimed to assess the beta diversity of fish assemblages and the relative importance of spatial and environmental filtering within a period of prolonged drought. Samples were collected with trawl nets in five reservoirs in July, September, and November 2016 and March and June 2017. Beta diversity based on taxonomy and abundance was divided into species replacement and differences in richness/abundance. Limnological variables and geographic distance between reservoirs were used to test their effect on fish assemblages. Abundance decreased and taxonomic beta diversity increased in the month of lowest volume, due to geographic isolation (spatial filtering), which may have limited dispersal and caused the clustered distribution of fish. Both components of beta diversity were important in explaining it, demonstrating the need for different conservation strategies. Therefore, conservation strategies need to be adopted to conserve fish and ensure recolonization of fish assemblages during the subsequent rainy season, reducing local extinction events.