A numerical model which simulates the propagation of waves over a complex bathymetry where the bottom contours are not straight and parallel, has been developed. In the model, the combined effects of refraction and diffraction can be considered. It is assumed that waves are linear, harmonic, and irrotational, and the effects of currents and reflection on the wave propagation are negligible. Mild slope equation is modified, assuming that there is no energy propagation along the wave crests, however, the wave phase function changes to handle any horizontal variation in the wave height. In this manner, the disadvantage of the parabolic approximation that one grid coordinate should follow the dominant wave direction, which causes problems in complex bathymetries, has been overcome. The finite difference method has been selected as the solution method. Applied methodology allows the check for breaking. Model results are compared with those from laboratory experiments published in the literature, and model is applied to Marmara Sea.