Density of phytoplankton in stabilization ponds influences treatment performance. The study hypothesized that the phytoplankton community structure varies according to local and temporal changes and consequently influences the treatment of the effluent. Phytoplankton community structure in facultative and maturation ponds in central Brazil was analyzed to provide guidance on system operation and maintenance. Further, species density, abundance, diversity, richness, dominance and beta diversity were measured. The efficiency of the treatment was evaluated based on Biochemical Oxygen Demand (BOD). Additionally, a Canonical Correspondence Analysis (CCA) was used to investigate how physical and chemical variables influenced the composition of the most abundant species in the dry and rainy seasons and the microalgae that were most related to the removal of BOD. One hundred and sixty-eight taxa were recorded, and the most abundant classes in both ponds were Chlorophyceae and Cyanophyceae (40% potentially toxic). The maturation pond had greater adaptability in the rainy season, while the facultative pond was more flexible in the dry season. The best period of growth varied among species. In both ponds, Chlorella minutissima was the one which most contributed to the optimization of the treatment. Thus, identifying phytoplankton species and relating them to water quality parameters and weather can help to understand the ecological dynamics of wastewater treatment and provide useful information for the operation and maintenance of stabilization ponds.