Despite the importance of phytoplankton as a source of autochthonous organic carbon, only a few studies have explored the ecological determinants of phytoplankton community structure in lotic systems when compared with studies in lakes. Thus, the aim of this study was to assess the seasonal phytoplankton dynamics in two distinct streams located in an area of environmental protection in subtropical Brazil, and to identify the main drivers of community structure. Phytoplankton community and environmental variables were sampled on a monthly basis, between September 2012 and August 2013, in Apepu and Gualberto streams, located in Foz do Iguaçu, Paraná, Brazil. We verified that both streams presented a seasonal distinction regarding the precipitation levels. Regarding the others environmental variables (e.g., nutrients, light, temperature), a temporal similarity was observed in both streams. A high taxonomic diversity was recorded, including Bacillariophyceae, Euglenophyceae, Chlorophyceae and Zygnematophyceae as the most representative groups. Low abundance, richness and diversity were recorded in Apepu and Gualberto streams, while high equitability was recorded in both streams due to the uniform distribution of the species. Low variability of phytoplankton was recorded with high temporal similarity between the two streams. This study shows that the factors determining phytoplankton diversity and dynamics in Apepu and Gualberto streams are related not only to hydrological and limnological conditions, but also to the local characteristics of the streams, such as low depth and small extension.