In this study, when seawall or harbor gate is installed for coastal disaster prevention, a two-dimensional water analysis in the bay is carried out to consider the flood amount of river inflow and effect of harbor gate. The Yeongsan river and the port Mokpo area are selcected for the study region. Then, by analyzing the hydraulic characteristics of flood flow of the Yeongsan river, we analysed the compatibility of the results in the two-dimensional hydrodynamic model. A twodimensional water analysis were conducted for the four cases considering whether a arbor gate is installed or not, and whether the inland water boundary condition is considered or not, also with open sea boundary condition. The results of the two-dimensional water analysis shows that water level change near the port Mokpo area is mainly caused by the discharge of the estuary barrage of the Yeongsan river because the harbor gate was installed. In addition, it is revealed that the volume of reservoir created by the harbor gate and the estuary barrage is too much small compared to the volume of the discharge from the Yeongsan river. Therefore, when the harbor gate is installed in the open sea, we concluded that a flexible management between the harbor gate and the estuary barrage of the Yeongsan river is required. A initial water level of the bay and outflow from the harbor gate are proposed for disaster prevention in the coastal area of port Mokpo.