Evaluating distribution patterns of species and identifying underlying responsible factors are essential to advance the understanding of how communities are assembled and also to support more effective decision-making for conservation. We evaluated the occurrence of a nested distribution pattern of phytoplankton communities among 25 shallow coastal lakes in southern Brazil. We evaluated nestedness of the total community matrix and of classifications of taxonomic and morphologically based functional groups and correlated the observed nestedness with environmental and landscape variables. We also identified nested and idiosyncratic species and evaluated the response of each group of species to geographic and environmental gradients. The results indicated a low but significant degree of nestedness in phytoplankton species composition and in most of the taxonomic and functional classifications, which were mainly correlated with soluble reactive phosphorus, total dissolved nitrogen and coefficient of variation of area. Nested species were influenced by geographic distance, suggesting dispersal limitation; whereas the distribution of idiosyncratic species underlined the importance of stochastic events in the patterns of phytoplankton communities. Our results showed that nestedness of taxonomically based or morphologically based groups is driven by different environmental factors, emphasizing the importance of taking into account ecological differences between taxonomic and functional groups of phytoplankton.