This article focuses on a two-dimensional numerical model established to determine the seabed dynamic response in the region of a permeable submerged breakwater. The wave motion in this article is governed by the volume-averaged Reynolds-averaged Navier–Stokes equation, whereas Biot’s poro-elastic equation determines the seabed foundation. The water surface is recorded using the volume of fluid technique. In this study, the results for the two-dimensional seabed dynamic response for both the consolidation status and the dynamic wave-induced response status for the seabed foundation coupled with submerged breakwater are illustrated. The numerical results examined from the dynamic pore pressure, the effective stresses, the shear stress, and the seabed soil displacements revealed that the impact of dynamic response at the offshore zone/seaward on the seabed foundation is more developed than at the onshore zone/harbor side. Parametric results analysis as regards the effect of the wave, the seabed, and the submerged breakwater structure variation significantly affected the seabed foundation response coupled with the breakwater structure. The numerical outcome on the liquefaction potential shows that the seabed foundation is more seemingly to liquefy and happen approximately at the toe of the submerged breakwater under the wave loading.