The functional group (FG) approach is used to predict the response of the composition of phytoplankton species to changes in the environmental conditions. We assessed for the first time the dynamics of phytoplankton communities in a High-Rate Algal Pond (HRAP), implemented for the bioremediation of landfill leachate, and using morphology-based functional groups (MBFG), under the American tropics conditions. These groups were later correlated with the physical and chemical variables of the system. Water samples were taken for biological, physical and chemical analysis for seven months. In addition, phytoplankton biovolumes were estimated and a canonical correlation analysis was performed to explain the relation between physical and chemical variables and FGs. Subsequently, the HRAP treated a medium-age leachate characterized by high concentrations of nutrients. Four MBFGs were identified (IV, V, VI and VII). Group V, conformed by phytoflagellates, was found to be dominant during the entire study period. This group proliferate in environments with high concentrations of organic matter, while contributing to the transformation of the contaminants present in the leachate. The largest biovolumes of Groups V and VII occurred during periods of low water levels and dissolved organic carbon. Finally, we show that the MBFG technique may be useful in understanding the dynamics of the phytoplankton community in the HRAP used for the treatment of landfill leachate.