The zooplankton community structure was examined in the Seomjin River-Gwangyang Bay Estuary in 2022. Zooplankton, which are sensitive to environmental factors, are effective bioindicators of ecosystem health in estuarine ecosystems, where physicochemical gradients influence community composition. Seasonal sampling demonstrated clear spatial variations in zooplankton abundance, highlighting the differing density trends observed between the riverine and bay stations. The Seomjin River stations exhibited lower densities in May than in September, whereas the Gwangyang Bay stations displayed the opposite trend. Copepods dominated the zooplankton assemblage, representing over 60% of the total abundance across all sampling sites in both seasons. Species-specific distribution, with varying dominant copepod species across the station in May, whereas Acartia omorii and Paracalanus parvus s.l. dominated the Seomjin River and Gwangyang Bay stations, respectively, in September. Nonmetric multidimensional scaling showed spatial differences that exceeded seasonal variability in structuring community composition. Correlation analysis revealed relationships between the distribution of copepods and environmental factors. This study provides baseline data on zooplankton distribution and community ...