Abstract: Ecological succession is vital for forecasting ecosystem responses to environmental changes and their future states. Zooplankton, a primary natural food source in aquaculture, plays a crucial role in maintaining ecosystem function. Thus, understanding how zooplankton communities respond to environmental changes is essential for economic and ecological outcomes. In this study, we examined three types of aquaculture ponds (crab, crayfish, and fish ponds) with over 10 years of history and analyzed 27 environmental factors potentially influencing zooplankton dynamics throughout the year. Our results showed that Rotifera was the most abundant group in all three pond types, followed by Protista, Cladocera, and Copepoda. The dominant species across different seasons and ponds were Polyarthra vulgaris, Anuraeopsis fissa, and Trichocerca pusilla. The alpha diversity of zooplankton was influenced by various environmental factors across different pond types, with significant effects of antibiotics observed only in the fish ponds. The temporal and spatial distributions of zooplankton communities varied significantly. Deterministic processes, driven primarily by temperature and ammonia nitrogen, were identified as the primary mechanisms influencing zooplankton community assembly in freshwater aquaculture ponds. These findings inform management practices aimed at regulating key environmental drivers and optimizing zooplankton dynamics, with implications for maintaining ecosystem stability and productivity and, ultimately, supporting sustainable aquaculture.