This study investigated the spatial distribution of dissolved organic carbon and the changes in tidal flat soil characteristics following the flooding season in the closed estuary of the Geumgang River basin. We found that after the flooding season, a brackish water area expanded due to increased river discharge, which also introduced low concentrations of dissolved organic carbon from the river. Dissolved inorganic carbon predominantly originated from the sea in proportion to salinity, indicating that in the closed estuary area, dissolved carbon supplied from the sea remained a significant source even after the flooding season. Additionally, a substantial amount of tidally transported silt and clay was deposited near the estuary dam after the flood, and its effects continued to influence the sediment characteristics downstream in the intertidal zone. As an empirical study in the closed estuary, our results are expected to contribute to conservation measures for the World Heritage Site in the area.