An effective way to access processes of ecological communities and ecosystems is the use of functional traits; therefore, the use of the functional characteristics of diatoms in paleolimnological works has been growing. In this study, the variations in the abundance of functional traits of sedimentary diatoms were evaluated in two lakes (Garças Lake and Patos Lake), from a subtropical floodplain, which present different intensities of influence of dams. Diatom community functional diversity and functional beta decomposed were calculated. A core from each environment was collected and samples of approximately 50 years were used. According to the functional diversity results, the two lakes showed different patterns, with a greater functional variation in Garças Lake. Through functional beta diversity results, the lakes showed similar results. Both showed a reduction in the functional diversity values and substitution of traits, after the 1980s in Garças Lake, and after ~ 2008 in Patos Lake. In these periods, both environments showed dominance of the same functional categories related to high turbulence and lower waters. The results suggest hydrological changes in the two lakes, which may have been driven by dams close to the floodplain.