This paper presents a numerical model for simulating wave interaction with porous structures. The model calculates the mean flow outside of porous structures based on the Reynolds averaged Navier-Stokes equations. The corresponding turbulence field is modeled by an improved k-e model. The flow in porous structures is described by the spatially averaged Navier-Stokes equations. The drag forces caused by the presence of a solid skeleton are modeled by the empirical linear and nonlinear frictional forms. The numerical model is first calibrated by simple experiments for flow passing through a porous dam with different porous media. Excellent agreements are obtained for the case using gravels with mean sizes of O (1cm) to O (10cm) as the materials for the porous dam. Reasonably good agreements are also obtained when small uniform glass beads with diameters of 3 mm are used. The calibrated numerical model is then employed to investigate the breaking wave overtopping a caisson breakwater, protected by a layer of armor units. Good agreements between numerical results and laboratory data are obtained in terms of both free surface displacement and overtopping rate. Different design scenarios are also studied numerically. The porous armor layer is effective in reducing the overtopping rate as well as in preventing the caisson breakwater from bottom scouring.