Aim Based on a study comprising water reservoirs within the Brazilian Cerrado biome, we seek to answer the following question: how does phytoplankton communities respond to environmental, landscape, and spatial predictors? We expected local predictors to be the main factors structuring the communities. Since phytoplankton has high dispersal capacity, the geographical distance would be of minor importance. Methods: We collected phytoplankton samples from 40 water reservoirs in the rainy season and 37 reservoirs in the dry season. We performed a partial Redundancy Analysis (pRDA) to evaluate the factors influencing the variation in the composition of phytoplankton communities. Results We found that spatially structured environmental factors were controlling phytoplankton communities at the rainy season, whereas landscape was the main predictor in the dry season. On the other hand, phytoplankton morphofunctional groups were influenced only by local predictors. Conclusions We demonstrated that phytoplankton dynamics differs between rainy and dry seasons, and that distinct predictors affect phytoplankton communities over seasons.