This research develops a two-dimensional numerical model for the simulation of the flow due to a solitary wave passing over a trapezoidal submerged breakwater on the basis of generalized vortex methods. In this method, the irrotational flow field due to free surface waves is simulated by employing a vortex sheet distribution, and the vorticity field generated from the submerged object is discretized using vortex blobs. This method reduces the difficulty in capturing the nonlinear deformation of surface waves, and also concentrates the computational resources in the compact region with vorticity. This numerical model was validated by conducting a set of simulations for irrotational solitary waves and then compared with the results of a relevant research. The comparisons exhibit good agreement. The rotational flows induced by different incident wave height were simulated and analyzed to study the effect of vorticity on the deformation and the breaking of solitary waves.