Phytoplankton functional classification based on simple morphological traits may simplify our understanding of variation in this community as a function of environmental filters. We tested the effectiveness of the morphology-based functional group (MBFG) approach as a model of phytoplankton temporal dynamics in a Brazilian subtropical river. The São João River has an area of approximately 79.10 km2, with 28.09 km2 located within the Iguaçu National Park, in Foz do Iguaçu, Paraná, Brazil. We collected phytoplankton samples and measured environmental variables in the intermediate river section on a monthly basis between August 2008 and July 2009. We tested for differences between the environmental variables, phytoplankton biovolume and sampled months and identified the environmental variables with the greatest influence on MBFGs. Our results revealed clear temporal variability of environmental conditions in this river. We recorded the presence of seven MBFGs (I, II, III, IV, V, VI and VII) in the lotic environment, with MBFG IV (chlorococcal chlorophyceans and desmids), V (flagellates) and VI (diatoms) being the most frequent and most important groups for phytoplankton biomass. Significant temporal differences were found for MBFGs I, II, IV, V and VI, with a clear seasonal succession, especially among MBFGs V and VI. Temperature, pH, electrical conductivity, transparency and nutrients were the main predictors of MBFGs in the São João River. Approaches based on traits have been increasingly applied in community ecology, and we believe that the MBFG approach can increase our understanding of environmental dynamics as well as improve the assessment of general ecological issues.