A smoothed particle hydrodynamic (SPH) model is developed to simulate wave interaction with porous structures. The mean flow outside the porous structures is obtained by solving Reynolds Averaged Navier-Stokes (RANS) equations and the turbulence field is calculated by a large eddy simulation (LES) model. The porous flow is described by the spatially averaged Navier-Stokes type equations with the resistance effect of the porous media being represented by an empirical frictional source term. The interface boundaries between the porous flow and the outside flow are modeled by means of specifying a transition zone along the interface. The model is validated against other available numerical results and experimental data for wave damping over porous seabed with different levels of permeability. The validated model is then employed to investigate wave breaking over a submerged porous breakwater and good agreements between the SPH model results and the experimental data are obtained in terms of free surface displacement. In addition the predicted velocity, vorticity and pressure fields near the porous breakwater and in the breaking wave zone are also analyzed.