A three-dimensional numerical model of water circulation has been developed. The model employs the equations on $sigma$-coordinate and the finite element method for numerical integration. To verify accuracy of the model, a series of numerical experiments have been conducted. The experiments include wind-driven currents in an one-dimensional channel, wind-driven currents in a square lake, and tidal current distributions in Masan-Jinhae Bay. The simulation results showed good agreements with the analytic solutions for wind-driven current and the field data sets in Masan-Jinhae Bay. The model can be used widely for modeling of water circulation in the waters with a complex geometry.