Circulation in the Jinhae Bay in the southern sea of Korea is examined using the Princeton Ocean Model (POM) with a free surface in a sigma coordinate, governed by primitive equations. The model well corresponds to the time series of the observed velocities at several layers obtained from a long-term mooring observation. In the residual velocity field of the model, persistent downward flow fields are formed along the central deep regions in the bay, and they are caused by bottom topographic effect. In addition, a comparison between a depth-averaged (2D) model and the POM is given, and a dependance of the results on bottom drag coefficient is also examined.