Evaluation of the relative influences of environmental and spatial processes in structuring aquatic metacommunities is an essential first step for understanding how these factors govern species distributions and affect spatial and temporal variability in community structure. Such variability has many causes and consequences at different scales. In the case of phytoplankton metacommunities, both species sorting and mass effect processes are likely to be important in structuring the patterns of biomass distribution on large spatial scales. We investigated the influences of environmental and spatial components on the phytoplankton community on a large spatial scale, consisting of a reservoirs‐river‐floodplain lakes gradient in a Neotropical region. Using partial redundancy analysis, we partitioned the relative role of environmental (environmental filters) and spatial (asymmetric eigenvector maps) processes structuring phytoplankton biomass. A clear difference of the limnological conditions was observed between the reservoirs and river–floodplain lakes system. High species richness and higher mean values of phytoplankton biomass were recorded in the floodplain lakes. Variation partitioning demonstrated the importance of both environmental and spatial process in phytoplankton biomass structuring. However, the relative importance of these processes may vary over time. Our results suggest that from a metacommunity perspective, the phytoplankton biomass of upstream reservoirs and a downstream river–floodplain lakes system is determined by environmental conditions (species sorting process), mainly in the floodplain lakes; and by high dispersion rates favoured by the connectivity and unidirectional flow (mass effect process), mainly between the reservoirs and the river.

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