To determine the effect of a waste stabilization lagoon discharge on the plankton in a receiving stream, bacterial and phytoplanktonic communities were studied above and below the outflow. The discharge apparently had seasonal and continuous effects on both the structure and function of plankton communities. These effects below the lagoon resulted in a significant increase in the bacterial and phytoplanktonic biomasses and significant changes in the structure of these communities: increases of Euchlorophyceae (Chlorella and Scenedesmus), Euglenophyceae (Trachelomonas), Cyanobacteria biomasses, and the relative biomass of very large bacteria. Metabolic activities of the plankton communities seemed to be significantly influenced; photosynthetic and heterotrophic activities increased, while productivity (photosynthetic assimilation and chlorophyll a) decreased. This decrease shows that allochthonous phytoplankton photosynthetic efficiency is lower than that of the autochthonous community or that this efficiency is reduced in the receiving stream. Discharge favored the development of mixotrophic microorganisms to the detriment of photosynthetic microorganisms.