In this paper an incompressible Smoothed Particle Hydrodynamics (ISPH) method is applied to investigate the flow motion in and around the porous structure. In order to describe in a simple and effective way the flow through the interface between the porous region and pure fluid region within the SPH framework, a heuristic boundary treatment method has been proposed. The ISPH model is first verified against a theoretical model of wave propagation over a porous bed and then further validated by comparing the predicted wave surface profiles and flow velocity fields with the experiment data for a typical case of flow motion around and inside a submerged porous structure. The good agreement has demonstrated that the improved ISPH model developed in this work is capable of modelling wave interaction with porous structures.