In this paper we present a new numerical modelling approach for coastal and marine applications where a porous media conceptual model was combined with a free surface volume-of-fluid (VOF) model and an immersed boundary method (IBM). The immersed boundary model covers the method of describing a solid object in a simple computational mesh without resolving the object with a conventional body-fitted mesh. This model enables a detailed resolution of some parts of a stone cover layer for erosion protection with the IBM model while other parts are handled with the conceptual porosity model. In this paper, the model is applied to investigate two practical cases in terms of a cover layer of stones on a flat bed under oscillatory flow at different packing densities, and a rock toe structure at a breakwater.