The Boussinesq equation model has been applied to compute the wave height and period in shallow water. The wave diffraction and refraction phenomena can be handled in the model at same time. The nonlinearity and dispersiveness of shallow water wave can be also evaluated in the Boussinesq model. In the paper, the computation method to resolve the Boussinesq equation by the finite difference approximation is introduced. The applicability of computation method for beach topography with a breakwater, a circular reef and a submerged breakwater is disscussed. The comparisons of the estimated wave heights with the measured ones in the model tests demonstrate the validity of computation model.