Resumo. Abstract Aim: The objective of this study was to evaluate the efficacy of phytoplankton functional groups as indicators of environmental conditions in floodplain rivers and lakes with different trophic state and connectivity degree to the Paraná River. Phytoplankton functional groups (FGs) cluster sensitive species to environmental variation and can be an alternative for environmental monitoring. Methods Samples were performed quarterly from 2010 to 2013 in the Ivinhema, Paraná and Baia Rivers and in three lakes permanently connected to each river. Results 419 taxa were identified, and those taxa that had values greater than 5% of the total biovolume were classified into FGs (P, C, A, B, MP, H1, W1, J, TD, LO, and N). The lakes presented higher biovolume and were more productive than rivers, especially in the dry periods. The rivers presented light limitation and low phytoplankton development. The FG LO was an indicator in rainy seasons. Both rivers and lakes were mostly oligotrophic. We registered FG indicators only for the lakes (A, B, C, E, LO, P, and W1) and mesotrophic environments (A, B, C, E, J, LO, and P). Conclusion The FGs reflected the seasonal variation and the trophic state of environments in the upper Paraná River floodplain, mainly in the lentic environments. The species-environment relationship (FGs as indicators) was clearer in the lakes, probably because of the longer water retention that allows evidencing the response of the phytoplankton community to environmental factors. On the other hand, the absence of FGs as indicators in the rivers could be due to the high water flow that promotes dispersal stochasticity and masks the relationship between the environmental factors and the phytoplankton community. Thus, phytoplankton FGs proved to be a viable tool to evaluate the environmental conditions in a floodplain.