The coupled-mode model developed by Belibassakis and Athanassoulis (J Fluid Mech 531:221-249, 2005) is extended and applied to the hydroelastic analysis of threedimensional large floating bodies of shallow draft lying over variable bathymetry regions. The method is also applicable to the problem of wave interaction with ice sheets of small thickness. A general bathymetry is assumed, characterized by a continuous depth function, joining two regions of constant, but possibly different, depth. We consider the scattering problem of harmonic incident surface waves, under the combined effects of variable bathymetry and a floating elastic plate of orthogonal planform shape. Under the assumption of small-amplitude waves and plate deflections, the hydroelastic problem is formulated within the context of linearized water-wave and thin elastic-plate theory. To consistently treat the wave field beneath the elastic floating plate, down to the sloping bottom boundary, a complete, local, hydroelastic-mode series expansion of the wave field is used, enhanced by an appropriate sloping-bottom mode. The latter enables the consistent satisfaction of the Neumann bottom-boundary condition on a general topography. Numerical results concerning floating structures over flat and inhomogeneous seabed are presented, and the effects of wave direction, bottom slope and bottom corrugations on the hydroelastic responses are discussed.