Due to its natural environmental advantages, the lagoon has become a significant fish farming area, with zooplankton playing a crucial role as bait for fish. The population dynamics of zooplankton are closely correlated with environmental variables in the lagoon. Therefore, it is necessary to analyze the population characteristics of zooplankton in different areas within the lagoon to understand the impact of environmental variables on their population structure. Through an analysis and study of fixed-point sampling in the Xincun Lagoon, it was observed that copepods dominated the species composition of zooplankton, accounting for 37.00% of the total number of species. Additionally, there were high numbers of planktonic larvae, primarily reflected in the composition of dominant species. On the other hand, the abundance of jellyfish was linked to anthropogenic pollution in the lagoon water environment. The analysis of environmental variables revealed that the Xincun Lagoon had severe DIN and DIP pollution. DIP and salinity also emerged as important factors influencing the distribution of zooplankton populations in the lagoon. Notably, the biomass, abundance, and diversity indices of zooplankton in the fish farming area were significantly lower than those in the lagoon mouth waters. This result suggests that the eutrophication in the Xincun Lagoon has exceeded its self-purification capacity and is deteriorating. The findings of this study highlighted the importance of long-term monitoring of zooplankton and environmental variables in the Xincun Lagoon, as well as active intervention measures, to promote the sustainable development of aquaculture in the lagoon.