Although some efforts have been made to understand the role of hydrology in structuring aquatic systems, little is known about how rainfall affects the relative roles of local environmental and spatial processes in structuring plankton metacommunities in tropical drylands. We hypothesize that the role played by spatial variables is more important in the dry than in the rainy season, because drought increases lakes isolation in semiarid regions. To test our hypothesis, we compared the variation in plankton structure between seasons attributable to local and spatial predictors by using variation-partitioning techniques. We used data for phytoplankton and zooplankton communities as a whole and separately by their size groups (nanoplankton, microplankton and mesoplankton) from 40 man-made lakes in northeastern Brazil. Our results showed that rainfall homogenized limnological variables and reduced total phytoplankton and nanophytoplankton beta diversity, but no effect of season was observed for microphytoplankton and zooplankton communities. Overall, in the dry season, both environmental and spatial variables were important structuring factors for the total phytoplankton, total zooplankton and microzooplankton communities, concurring with both niche- and neutral-based models. In the rainy season, spatial variables were neither important for shaping the phytoplankton nor the zooplankton metacommunities, confirming our hypothesis. The main ecological implication of our findings is that both niche- and neutral-based processes might play an important role on phytoplankton and zooplankton metacommunities dynamics in a future warmer and drier climate in tropical semiarid regions.