To elucidate the species compositions of estuarine and inshore fauna and compare productivities between them, catch were collected by bag nets in the Han River estuary off Ganghwa Island and the inshore waters off Jangbong Island for 24 hours at the spring tide from March to December 2010. Community structures of nekton assemblages were different with area, month, taxonomic groups. Although the diversity of estuarine nekton assemblage was lower than that of inshore nekton assemblage, the productivity of nekton assemblage in estuary was higher than that in the inshore waters. Nekton assemblages were distributed according to habitat environment: the estuarine species, Coilia mystus, Chelon haematocheilus, Collichthys lucidus were prominent in the Han River estuary off Ganghwa Island, and marine species, Thryssa kammalensis, Sardinella zunasi, Portunus trituberculatus were prominent in the inshore waters off Jangbong Island. Palaemon gravieri, Exopalaemon carinicauda, Synechogobius hasta were inhabited in both waters. The health assessment of estuarine ecosystem based on scientific research will be contributed to the effective management of estuary with determination of order and direction in policy.