The economical design of rubble mound structures namely breakwaters can be facilitated by means of an accurate simulation of interactions between the porous media and the passing currents and waves, to assure the safe economical design of these structures. Unlike most of the previous studies, the present study dealt with the development of a more realistic simulation by simultaneous consideration of the porous structure reshaping and the fluid flow interactions. To this end, the wave interactions with the porous media together with the breakwater deformation are modeled using a combination of FVM-VOF-DEM numerical methods. The flow in both the pure fluid and porous media were modeled using a new formulation of an Eulerian FVM-VOF method, while a Lagrangian DEM method with a new simple porosity adjustment was incorporated to simulate the deformation of the breakwater. The performance of the presented model is evaluated by comparing its results with those of laboratory measurements. The results indicate that the developed model can accurately simulate the free surface and the flow passing through the porous media; as well as the breakwater deformation.