Resumo. Abstract In impacted floodplains, small tributaries have an essential role in the maintenance of ecosystem biodiversity. Aim: We aimed to characterise the periphytic diatom community (Bacillariophyta) in a protected area at the Upper Paraná River floodplain considering the importance of tributaries as a source of propagules. The purpose of this study was to understand the influence of the tributaries in the periphytic diatom community (Bacillariophyta) in a protected area at the Upper Paraná River floodplain. We expect that species present in the main river channel (mainly in the last stretch) would be a subset of the community present in the tributaries. Methods The study area is located in the last non-dammed stretch of the Paraná River in this floodplain, with the contribution of several tributaries. Sampling was performed in 2014 in two tributaries and three sites at the Paraná River main channel, and the periphytic material was obtained from petioles of the aquatic macrophyte Eichhornia azurea (Sw.) Kunth. Results We identified 115 diatom taxa. Higher values of species richness were registered in the tributaries, and higher densities in the tributaries and at sampling sites under the direct influence of the tributaries. We also observed a higher similarity between the tributaries, which are located in the preserved side of the floodplain. The results of beta diversity showed that closer sites had lower values, and that the species turnover was the component more important in this floodplain. Conclusion In this way, these results reinforce the importance of tributaries mainly on the algae establishment and development reflected in the density of species. It demonstrates that sites in preserved area present a higher species richness and can serve as a pool of propagules for downstream environments.