Drought events will become more frequent due the climate change. In floodplains, periphytic algae are responsible for part of the primary production, are the principal source of organic carbon deposition, play an important role in mineralization and nutrient cycling, and are the base of the food web for many organisms. As algae distribution in aquatic environments is a strong indicator of physical and chemical conditions of the sites, we aimed to determine the structure of periphytic algae in lentic and lotic environments during drought conditions and to uncover the main local abiotic factors in community structuring. We hypothesized diatoms would be more frequent than green algae and desmids at both sites, due to their resistance characteristics, and that higher periphyton algal richness, density and diversity would occur in the lake due to the greater availability of nutrients and the absence of flow. The study was carried out in the Finado Raimundo lake and the Ivinhema river in the Upper Paraná river floodplain during the low water period of 2011. Petioles of the aquatic macrophyte Eichhornia azurea (Sw.) Kunth were used as a substrate for periphytic algae. We found a total of 171 species, 104 species in the lake and 80 in the river. Diatoms were predominant at both sites due to their strategic traits, and between sites, there were different patterns in the periphytic algal community structure, owing to the distinctive physical and chemical characteristics of the lake and the river. Achnanthidium minutissimum (Kützing) Czarnecki and Nitzschia palea (Kützing) W. Smith were the most abundant species in both environments. Our results showed patterns of periphytic algae in a floodplain during drought conditions, which will assist in understanding their structuring during future drought scenarios.