An advanced second moment closure for rough wall turbulence is proposed. In contrast to previously proposed models relying on an empirical correlation based on equivalent sand grain roughness, the proposed model mathematically derives roughness effects by applying spatial and Reynolds averaging to the governing equations. The additional terms in the momentum equations are the drag force and inhomogeneous roughness density terms. The drag force term is modeled with respect to the plane porosity and plane hydraulic diameter. The two-component limit pressure-strain model is applied to the additional pressure-strain term, which is related to the external force terms. An evaluation of turbulence over surfaces with randomly distributed semi-spheres confirms that the developed model reasonably reproduces the effects of roughness on mean velocity, Reynolds stress, and energy dissipation. Turbulence over rough surfaces of marine paint is also simulated to assess the predictive performance for higher Reynolds number turbulent flows over real rough surfaces. The developed model successfully reproduces the dependence of the Reynolds number on roughness effects. Moreover, qualitative agreement of the skin friction increase with the experimental data is confirmed.