The Ariake Sea, a typical semi-closed bay located in Kyushu Island, western Japan, has a maximum tidal range of 6m in spring tide and vast tidal flat. Recently, the Ariake Sea attracts considerable public attention, because its fishery environment is becoming worse. Especially, oxygen-deficient water mass and red tides often emerge in summer season and result in severe bioenvironmental deterioration. To simulate and understand these phenomena, a threedimensional analysis is strictly needed because the vertical mixing process of water mass is one of the fundamental factors for these phenomena. In modeling the vertical mixing process in coastal waters, the Princeton Ocean Model (POM) , which is a widely used threedimensional ocean model with a terrain-following sigma-coordinate system, is suited to the shallow coastal oceans. This coordinate system has the same number of levels everywhere in the ocean, irrespective of the depth of water column. In this study, the POM was applied to the numerical simulations of tidal current in Isahaya Bay located in the western part of the Ariake Sea. A wetting and drying scheme was incorporated into the POM to reproduce submergence at high water and emergence at low water of tidal flat. The results indicated that the POM was able to approximately predict the observations of tidal current in Isahaya Bay. It was concluded that the POM could be used in the numerical simulations considering the effects of temperature, salinity, wind forcing and freshwater fluxes in the next step of this study.