This study was conducted for the understanding of zooplankton community structure and energy flow in Yongsan River estuary through the analysis on the seasonal community structure and the measurements of growth rates of dominant copepod Paracalanus parvus s. l.. Field survey was carried out at 7 stations near Yongsan River estuary in May, July, September, and November 2008. Meso-zooplankton communities were composed of 22 taxa in this study period. The spatial variations of species compositions showed a relatively identical distribution regardless of season. This distribution pattern was resulted from the weak effects of the spatial salinity variations that is known to be an important factor for the determination of spatial zooplankton distribution in estuary. The zooplankton communities in this study waters could be generally characterized by the typical coastal-estuarine community structure that was comprised with a few dominant species and abundant density. The mass occurrence of Noctiluca scintillans in May suggested that the environmental situation was unstable due to the geological features and active anthropogenic impacts in Yongsan River estuary. The seasonal average growth rates of dominant copepod Paracalanus parvus s. l. showed a narrow range from 0.12 to 0.15 day−1. However, The spatial variations of growth rates showed that the growth rates near Yongsan River estuary barrage were continuously higher than those at outer stations throughout the year. This results suggested that the growth of copepod was a food-dependent in Yongsan River estuary.