Integrated assessment of the water environment has become widespread in many rivers, lakes, and reservoirs; however, aquatic organisms in freshwater are often overlooked in this process. Zooplankton, as primary consumers, are sensitive and responsive to changes in the water environment. Water and zooplankton samples were collected on-site at Shanxi Reservoir quarterly to determine 12 water environmental indicators and to quantify the abundance of zooplankton of Cladocera, Copepoda and Rotifera by using the ZooScan zooplankton image-scanning analysis system, combined with OLYMPUS BX51 using machine learning recognition classification. The aim was to explore the relationship between water environmental factors and zooplankton through their spatial and temporal heterogeneity. Through principal component analysis, redundancy analysis and cluster analysis, variations in the factors driving zooplankton population growth in different seasons could be identified. At the same time, different taxa of zooplankton can form clusters with related water environmental factors during the abundant water period in summer and the dry water period in winter. Based on long-term monitoring, zooplankton can be used as a comprehensive indicator for water environment and water ecological health evaluation, as well as providing scientific support for regional water resources deployment and management.