An implicit baroclinic three dimensional numerical model (HIDROTAM-3) has been developed to simulate the transport processes in coastal waters. Model has hydrodynamic, transport and turbulence model components, and it can simulate transport processes due to the tidal or nontidal forcing which may be barotropic and baroclinic. The two equation k- modeling has been tested in the turbulence modeling. It is a composite finite difference-finite element model. In the horizontal plane, second order central finite differences on a staggered scheme and in the vertical Galerkin Method with linear shape functions are used. Implicit equations are solved by Crank Nicholson Method, which has second order accuracy in time also. Developed model whose predictions are compared with the analytical solutions, has been applied to Bay of Fethiye located on the Mediterranean Coast of Turkey, where the dominant forcing for the water exchange is due to the wind action. To control the predictions of the numerical model, a field study has been carried out in the Bay and continuous measurements of velocity have been taken throughout the water depth at different locations. Model predictions are in good agreement with the field data.