In the usual linear wave-body interaction problems, the variation of the space-wise mean level of the free-surface is ignored and the free-surface boundary condition is imposed on the calm water-surface level. In some problems, however, the variation of the mean free-surface displacement can be so large that it can no longer be ignored even in a linear theory. In the present paper, the formulation that accounts for such effect is presented. As an example application of the presented formulation, the water-surface displacements associated with an oil recovery ship, part of which consists of a water-way bounded by a shallow bottom plate, are computed and compared with experimental results.