A double-body 3D potential-flow code developed earlier for computing hydrodynamic interaction forces and moments acting on the hulls of the ships sailing in close proximity with neighboring ships or some other obstacles, is extended to the shallow water case. Two methods for accounting for the finite water depth were implemented: (1) using truncated mirror image series and (2) distribution of an additional single layer of sources on parts of the seabed beneath the moving hulls. While the first method does only apply to the flat horizontal seabed, the second one can also deal with the arbitrary bathymetry situations. As appropriate choice of the discretization parameters can significantly affect the accuracy and efficiency of the second method, the present contribution focuses on comparative computations aiming at defining reasonable dimensions of the moving paneled area on the sea bottom and maximum admissible size of the bottom panel. As result, conclusions concerning optimal parameters of the additional set of panels are drawn.