An integrated two-dimensional vertical (2DV) model was developed to investigate wave interactions with permeable submerged breakwaters. The integrated model is capable of predicting the flow field in both surface water and porous media on the basis of the extended volume-averaged Reynolds-averaged Navier–Stokes equations (VARANS). The impact of porous medium was considered by the inclusion of the additional terms of drag and inertia forces into conventional Navier–Stokes equations. Finite volume method (FVM) in an arbitrary Lagrangian–Eulerian (ALE) formulation was adopted for discretization of the governing equations. Projection method was utilized to solve the unsteady incompressible extended Navier–Stokes equations. The time-dependent volume and surface porosities were calculated at each time step using the fraction of a grid open to water and the total porosity of porous medium. The numerical model was first verified against analytical solutions of small amplitude progressive Stokes wave and solitary wave propagation in the absence of a bottom-mounted barrier. Comparisons showed pleasing agreements between the numerical predictions and analytical solutions. The model was then further validated by comparing the numerical model results with the experimental measurements of wave propagation over a permeable submerged breakwater reported in the literature. Good agreements were obtained for the free surface elevations at various spatial and temporal scales, velocity fields around and inside the obstacle, as well as the velocity profiles.