We carry out a numerical calculation to understand the nonlinear wave deformation around breakwaters using the Boussinesq equation, which is weakly nonlinear and weakly dispersive shallow water equation. A numerical method based on a finite element scheme and fourth order Runge-Kutta algorithm is employed to investigate the diffraction of incident waves by the breakwater. As a computational model, two-dimensional wave flume is treated. The breakwaters is perpendicular to the side wall of a channel. From the numerical results, the wave deformations according to the change of the length and the thickness of breakwaters are investigated. We also investigate the effect of the nonlinearity by comparing the results with the linear solutions.