Temporal and spatial variation in the freshwater region, created by river runoff, of a small bay, caused by the passage of typhoons was examined using a three-dimensional primitive equation model (the Princeton Ocean Model, POM). Numerical experiments were implemented focusing on temporal evolution in the freshwater region in association with typhoon tracks. The model domain covered most of the estuary around the Nakdong River, including Noksan Bay, where river water is periodically released from upstream (Noksan dam). The model showed that the extension of the freshwater region outside of the bay depended strongly on the tracks of typhoons, specifically the associated wind directions and inner flow fields that are accompanied by new clockwise eddies. The model also showed that entrainment from typhoon passage frequently creates salt wedges in the estuary, indicating that organisms in the bay are biologically and chemically influenced with variation in the freshwater region.