Funil Reservoir receives inflow from a highly industrialized region and acts as a natural sink to pollutants. Among the consequences of the uncontrolled nutrient loading is the constant presence and periodic heavy blooms of Microcystis aeruginosa. This study verified limnological features and zooplankton assemblage of the Funil Reservoir focusing on the environmental-indicator properties of rotifers and cladocerans. The summer bloom of M. aeruginosa caused reductions in water transparency, nitrate and orthophosphate concentrations and raises in chlorophyll a, pH, dissolved oxygen and chemical oxygen demand values. All zooplankton species presented spatial and temporal variations with the exception of the copepods, which were present in all samples. According to canonical correspondence analysis, ammonium was the variable most related to zooplankton variability and different Rotifera and Cladocera assemblages indicated distinct environment conditions. Rotifer taxa associated with increases of water temperature and chlorophyll a concentration were found with high densities during M. aeruginosa blooms. Species of rotifer and cladocerans are suggested as indicators that can be used to identify different physical and chemical gradients or eutrophic increases in Funil Reservoir.