To collect information about the community structure of zooplankton and to study how zooplankton respond to environmental conditions, zooplankton samples were collected from seven stations in a heavily polluted river (the Nanfei River, China). Samples were collected in March (spring) and June (summer) 2014, September (autumn) and December (winter) 2013. A total of 275 species of zooplankton belonging to 79 genera were identified, the total zooplankton abundance was 193 040 ind./L. Protozoa and rotifer comprised a high proportion of species number and abundance of zooplankton. The upper reaches had higher greater species number and lower abundance than those in middle and lower reaches, and at the entrance of Chaohu Lake. The species number and abundance of zooplankton were the highest in autumn, and the lowest in winter. The habitats of Nanfei River had high spatiotemporal heterogeneity, revealed by unweighted pair-group method using arithmetic averages (UPGMA) clustering analyses on environmental factors and detrended correspondence analysis (DCA) clustering analyses on zooplankton abundance. In addition, water quality of upper reaches was better than the middle and lower reaches, and the entrance; and better in autumn than in other three seasons in terms of species number, abundance, Shannon-Wiener index, and Pielou evenness index. Results of canonical correspondence analysis (CCA) indicate that the combination of water temperature, total phosphorus, total nitrogen, pH, chemical oxygen demanded, soluble phosphate, and conductance rate were responsible for the variations in zooplankton community structure. Results of the present study indicated that zooplankton communities of the Nanfei River had obvious spatial and temporal heterogeneity, and the environmental factors played an important role in the changes in zooplankton community in Nanfei River.