The evaluation of abiotic and biotic variables can provide information for understanding the structure and function of lotic systems. To obtain this information, measurements of 15 chemical and physical variables and of phytoplankton were conducted at two sampling stations. The present study aims to evaluate the temporal and spatial variation of planktonic diatoms in terms of abiotic variables and the trophic level of the river water and to select diatom species as descriptors of the physical and chemical conditions of the water upstream (S1) and downstream (S2) of the Iguassu River over an annual cycle. Sampling station S1 was classified as oligotrophic to mesotrophic, and S2 was classified as ultra-oligotrophic to oligotrophic. A total of 98 diatom species distributed among 39 genera was recorded, showing no dominant species but 36 abundant species. Although the differences of chemical and physical variables between S1 and S2 were limited to greater turbulence and turbidity, processes triggered by heavy rainfall exerted a significant influence on community structure, and a temporal change in composition was observed. At the end of the dry period, due to the recovery of nutrients and high transparency, there was an abundance of Cocconeis placentula var. lineata. In the rainy period, with increased turbulence and turbidity processes resulting from higher rainfall, there was an abundance of Aulacoseira granulata var. granulata.