We analyzed the 3-D characteristics of the dynamic response of seabed around a submerged breakwater due to wave loading using a 3-D numerical scheme (LES-WASS-3D). Using our model, which considers the wave-structure-sandy seabed interactions in a 3-D wave field, we were able to investigate the 3-D characteristics of the pore-water pressure in the seabed around the submerged breakwater under various incident wave conditions. To verify the 3-D numerical analysis method suggested in this study, we compared the numerical results with the existing experimental results and found good agreement between them. The numerical analysis reveals that high pore-water pressure in the seabed is generated below a large wave height at the front slope of the submerged breakwater. It was also shown that the non-dimensional pore-water pressure in the seabed increases as the wave period increases because the wave energy dissipation decreases on the submerged breakwater and seabed as the wave period increases.