Effect of turbulence modeling on the simulation of wind induced circulation patterns in coastal waters, has been investigated. Eddy viscosities are calculated by a two equation k-epsilon turbulence model, and by a two equation k-w turbulence model, that are commonly applied in modeling of coastal transport processes. Kinetic energy of turbulence is k, dissipation rate of turbulence is 6, and frequency of turbulence is w. In the modeling of turbulence by k-epsilon model and by k-w model, a composite finite element-finite difference method has been used. The governing equations are solved by the Galerkin Weighted Residual Method in the vertical plane and by finite difference approximations in the horizontal plane. The water depths are divided into the same number of layers following the bottom topography. Therefore, the vertical layer thickness is proportional to the local water depth. From the applications, it has been seen that application of two equation k-w turbulence model in the prediction of wind induced circulation in coastal waters leads to better predictions compared to k-w model.