Zooplankton are sensitive to changes in the water environment and can characterize the degree of water pollution. The zooplankton community structure in the Guishui River was investigated in 2017, the temporal and spatial variations in zooplankton community structure and their relationship with environmental factors were analyzed, and water quality was evaluated using biological evaluation methods. The results showed that there were 4 phyla, 22 genera, and 88 species of zooplankton in the Guishui River, dominated mostly by rotifers and protozoa (42 species), the average cell density and biomass of zooplankton being 5041.58 ind/L and 2.88 mg/L, respectively. CCA analysis between the zooplankton community structure and environmental factors showed that water temperature, pH, DO, and NH₃-N were important factors affecting changes in zooplankton community structure in the Guishui River, and the relation of Anuraeopsis fissa, Trichocerca lophoessa, and Keratella cochlearis to nitrogen and phosphorus is extremely significant in the water body. These species can be used as eutrophication indicators for monitoring water quality. The annual values of the zooplankton diversity index (H), evenness index (J), and richness index (D) of the Guishui River were 0.43, 0.31, and 0.41, respectively. The overall evaluation results showed that the Guishui river was at the level of medium to high eutrophication, especially in the urban areas which were highly polluted, indicating that the ecological function of the Guishui river was impaired, and that the water quality needed further improvement and treatment. The results of this study can provide a theoretical basis for water quality assessment, water environment monitoring, and water pollution control of the Guishui River.