Resumo. Abstract Aim: We analyzed the temporal distribution (dry and rainy periods) of phytoplankton functional groups (biovolume) from lakes connected to dammed (S1 - Paraná River) and non-dammed rivers (S2 - Baia River and S3 - Ivinhema River) in the upper Paraná River floodplain, Brazil. We also determined the drivers of the phytoplankton community assemblage. Methods Phytoplankton and environmental variables samplings were performed quarterly in dry (2000 and 2001) and rainy (2010 and 2011) periods. We classified the phytoplankton species into seven morphological based functional groups (MBFG). We used analysis of variance to test differences in total phytoplankton biovolume and MBFGs biovolume between lakes and climatic periods. We also used redundancy analysis to determine the MBFGs-environment relation. Results The lake related to the dammed river (S1) presented the lowest species richness. The total phytoplankton biovolume presented differences among the lakes, but we did not register temporal differences associated with water level variation. The lake related to the non-dammed and semi-lentic river (S2) presented the highest biovolume, while S1 (related to the dammed river) and S3 (related to the non-dammed river) exhibited the lowest ones. Filamentous organisms (MBFG III) were associated with poor nutrient conditions and diatoms (MBFG VI) were favored in high water mixing sites. The flagellate groups MBFG II and MBFG V were related to deeper water and lower column mixing conditions, respectively. Conclusions Our results suggest that phytoplankton species with different functional traits drive the primary productivity in the dry and rainy periods. Hence, we highlight the importance of maintaining high functional diversity in lakes to ensure primary productivity. Therefore, we stress the importance of protecting the natural environment such as floodplain lakes because of its contribution to the regional biodiversity and the flow of energy.