Accurate estimation of the wave-induced pore water pressure in the seabed is key factor in studying the stability of the seabed in the vicinity of coastal structure. Most of the existing numerical models for wave structure seabed interaction have been linked through applying hybrid numerical technique which is analysis method separating the wave field and seabed regime. Therefore, it is necessary to develope a numerical model f3r simulating accurately wave$cdot$structure$cdot$ seabed interaction under wave loadings by the single domain approach for wave field and seabed regime together. In this study, direct numerical simulation is newly proposed. In this model, modeled fluid drag has been used to detect the hydraulic properties according to the varied geometrical shape inside the porous media by considering the turbulence resistance as well as laminar resistance. Contrary to hybrid numerical technique, direct numerical simulation avoids the explicit formulation of the boundary conditions at the fluid/porous media interface. A good agreement has been obtained by the comparison between existed experimental results by hydraulic model test and direct numerical simulation results far wave $cdot$structure$cdot$seabed interaction. Therefore, the newly proposed numerical model is a powerful tool for estimating the nonlinear dynamic responses among a structure, its seabed foundation and water waves.