A coupled-mode model is developed and applied for the propagation of water waves in the presence of porous submerged breakwaters, in the form of a horizontal porous plate, over variable bottom topography. A parallel-contour bathymetry is considered, described by a continuous depth function, joining two regions of constant, but uneven, depth. Under the assumption of small-amplitude waves, the problem is formulated in the context of linearized water-wave theory. A local-mode series expansion is used for the unknown field, where the vertical eigenfunctions are derived using Darcy’s law for the porous medium. The modal series is enhanced by an extra mode, and a coupled-mode system is obtained for the unknown horizontal amplitudes. Proper boundary conditions are introduced enforcing complete matching of the field at the vertical interfaces with the regions of constant depth. Results are presented and discussed concerning the treatment of the complex dispersion relation and the effect of the seabed irregularity. The present model can be helpful for understanding the effect of the variable bathymetry on the design of submerged porous breakwaters.