The refraction-diffraction of surface waves due to porous variable depth has been the subject of many investigations. In the present study, we extend the boundary-value problem of impermeable varying topography to that of a variable depth porous seabed, which is the situation most likely to be encountered in practical problems of coastal engineering. A wave-induced fluid motion is applied to the porous bottom, while the well-known linear potential theory is applied to the free-water above the bottom. Eigenfunction expansions are employed to derive the matching condition and the so-called modified dispersion relation. As a result of the porous bottom, the wavenumber becomes a complex value, of which the real part represents the spatial periodicity while the imaginary part refers to the energy dissipation. The characteristics of water waves over a porous bottom are studied in detail. By neglecting the non-propagating modes which only have a local effect and damp exponentially with distance, we derive a mathematical model to represent the characteristics of both the wave refraction-diffraction and wave-damping. The developed model is applied to the damping problem of waves over submerged porous breakwaters.