Abstract. AIM: The uneven distribution of organisms in aquatic ecosystems is generally attributed to environmental heterogeneity in both space and time, reflecting the occurrence of appropriate environmental conditions and the availability of resources to biological communities. The aim of this study was to understand how the dissimilarity of the phytoplankton community in a large subtropical shallow lake is related to environmental dissimilarities. METHODS: Biotic and environmental data were gathered at 19 sites along the 90-km length of Lake Mangueira. Sampling was carried out quarterly during 2010 and 2011, totaling 152 sampling units. The relationship between phytoplankton dissimilarity and the dissimilarity of environmental variables was assessed by the BioEnv analysis. MAJOR RESULTS: There is a significant relationship between phytoplankton dissimilarity and environmental dissimilarity. The model that best explained the dissimilarity of phytoplankton among the sampling units included pH, turbidity and nitrate. CONCLUSIONS: The dissimilarity of phytoplankton was related to the dissimilarity, which were directly associated to the variability of conditions and resources in space and time in Lake Mangueira.