A numerical model of surface wave movement and water filtration in saturated-unsaturated porous medium has been developed. The model can be used to define the parameters of the wave run-up on the slope protected with a permeable fixed layer. The model is applied to determine positions of the free wave surface at the different times, including such parameters as the height of wave run-up and wave run-down on the slope. In addition, both flow velocity field in the upper protected layer and moisture distribution in the soil body of the slope were defined. The model is verified with the results of the published large-scale tests that have been conducted at Technical University Braunschweig in the wave flume with the slopes protected according to Elastocoast technology. The numerical model can be applied to calculate the run-up of extreme waves on protected engineering and beach slopes in natural conditions.