The structure of freshwater phytoplankton communities can be strongly influenced by environmental and spatial processes at different scales. To identify the main forces that drive phytoplankton structure becomes a relevant tool to understand several knowledge gaps in the phytoplankton ecology domain, such as community succession, biological invasions and responses to disturbances. We used the morphological-based functional groups (MBFG) approach to investigate the influence of environmental conditions (physical and chemical factors), nutrient availability and spatial processes (habitat connection and species dispersal) in structuring microphytoplankton community in a subtropical hypereutrophic reservoir located in southern Brazil. Samples were taken quarterly, between February 2017 and December 2018. We used distance-based multivariate analysis of variance (PERMA-NOVA) to evaluate potential spatial and seasonal dissimilarities in the MBFG's biovolume, and variation partitioning approach (pRDA) to evaluate the role of environmental, nutrient availability and spatial components in explain the microphytoplankton community structure. We identified 16 microphytoplankton taxa, which were sorted into five MBFGs. Significant seasonal dissimilarities were observed in the MBFG's biovolume. Higher relative biovolume of potential harmful cyanobacteria (MBFG III) and alien dinoflagellates (MBFG V) was observed in summer and autumn/winter, respectively. Pure environmental component (composed by physical and chemical predictors insolation, precipitation, total dissolved solids, turbidity, water temperature, water transparency and wind intensity) explained 45% of the variance in the MBFG's biovolume, whereas pure nutrient availability component explained 7% and spatial component explained only 3% of the biotic variance. The results showed that the environmental factorsespecially the seasonal-influenced onesare more effective than nutrient availability and spatial processes in explaining the microphytoplankton community structure in this ecosystem. Our findings alert to the need to consider the variability of the environmental conditions (mainly those directly influenced by seasonality) in phytoplankton community structure in disturbed freshwater ecosystems prone to eutrophication events.