Understanding spatial and temporal changes in species composition has long demanded the attention of ecologists. However, only recently questions related to changes in species functional traits have been investigated. We explored patterns of species and functional dissimilarity of periphytic algae at six lakes sampled over a year across a subtropical floodplain. We evaluated the importance of turnover and nestedness components across space and time; the influence of environmental dissimilarity, spatial distance, and time on species and functional dissimilarity; and whether functional dissimilarity results from nonstochastic assembly processes. We used six functional traits to describe 155 species. Functional dissimilarity was estimated by functional dendrograms, and stochasticity was evaluated using null models. The turnover component was greater than nestedness for species and functional dissimilarity. Environmental dissimilarity, spatial distance, or time did not significantly explain species or functional dissimilarity.However, functional dissimilarity was significantly greater than expected given the observed species dissimilarity. The main finding of this study is that community assembly was deterministic with respect to traits. Further, each lake contributed similarly to the overall species and traits pool. These results highlight the importance of comparing species and functional dissimilarities to reach a better understanding of the organization of periphytic algal communities.