Experimental measurements on a large-scale, multi-layered breakwater model are used to extensively validate a numerical model for wave interaction with permeable coastal structures, built in a generic multiphysics CFD code, FLOW-3D. A novel contribution to this code is the implementation of the piston-type wave-maker with active wave absorption. The use of active absorption is crucial to maintain an accurate and stable incident wave field in the validation test series with long duration. Due to the nonbreaking wave conditions, the model setup is simplified to two-dimensions and single-phase laminar flow in the clear-fluid region. The validation includes a verification of the incident wave field and a detailed study of the hydrodynamics of the flow field within the breakwater. The evolution of experimentally measured free-surface elevations in and outside the breakwater shows a good agreement with numerical predictions. Numerical results of pore pressure height throughout the breakwater core are generally corresponding well with experimental values, except for a limited zone near the free surface where a clear reduction of the pore pressure is measured, due to the effect of air entrainment. This validation study, using large-scale model tests, proves that this model, and by extension the nowadays standard branch of VOF-based Navier–Stokes models, are a useful tool in predicting wave interaction with permeable coastal structures. The study also reveals that it is possible to achieve a level of accuracy that can be considered sufficient for engineering applications, even when using some model simplifications, in particular those related to the treatment of the aerated turbulent flow on and inside the armor layer.