This study aimed to determine if there are any differences in the attributes and composition of the phytoplankton and epiphyton communities between organic (OF) and conventional (CF) rice fields. We also strove to identify if there were any variations in these communities by comparing samples taken from two different periods (12 and 35 days) after the application of the herbicide clomazone and penoxsulam in CF. The farms are located in the Pampa Biome, Southern Brazil. Phytoplankton samples from the subsurface water and epiphyton samples from the rice stems were analyzed using the Utermöhl method. The CF and OF had distinct environmental conditions (pH, conductivity, and turbidity values), and the residual concentration of the herbicides decreased over time. There were no significant differences in epiphyton and phytoplankton density, or in phytoplankton richness, between the rice fields; only the epiphyton richness and taxonomic composition showed differences between the rice fields. Cyanobacteria and Chlorophyceae comprised a large proportion of the epiphytic density in CF and OF, respectively. However, Bacillariophyceae and Chlorophyceae had greater phytoplankton densities in CF and OF, respectively. The taxonomic composition of communities should be considered an effective tool to show the differences between the two cultivation systems.