Residual current plays more important role than the tidal current for long-term material transport in coastal areas. The main component of residual current is tide-induced residual current. Otherwise, wind driven current and buoyancy-driven current are important components which change the residual current. To clarify the characteristic of coastal current, application of a three -dimensional model is necessary. This study focuses on clarifying the stratified systems of coastal water affected by freshwater runoff from a river and analyzes the structure of current at Ulsan bay by applying a three-dimensional buoyancy-driven current model. According to the result of “Ulsan bay” study, it shows that the surface layer in semi-enclosed estuaries, which affected by freshwater runoff. has flows going out, and the bottom layer has flows coming in. Besides when the wind blows toward inside of the bay, the surface layer has flows coming in and the bottom layer has flows going out as compensation flows for the surface circulation. The results of simulation could be applicable to examine vertical upwelling, which might be caused by construction of artificial fishing reef to build aqua farm, submerged breakwater to control coastal sediment, and the formulation of oceanic ridge, or a basic study on application to the usage of deep water.