Abstract: A new development of a three dimensional (3D) multi-layer wind-induced circulation model of Ariake Sea region is described in this study. The hydrodynamic equations are derived from 3D Navier Stokes equations and solved using the Fractional Step Method (FSM). The 3D hydrodynamic model is first tested against analytical solution in order to investigate the performance of the model. And then, it was applied to the Ariake Sea. For model test, the numerical results are almost identical to the analytical solutions. It was shown that the numerical model developed was capable to simulate wind-induce flows in shallow semi-enclosed/enclosed waters.