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This paper presents a potential flow solution for online estimation of hydrodynamic interaction between ships moving in restricted waters with complex boundaries. Each ship in concern is linked with a moving patch representing the arbitrary bathymetry beneath it. The wetted surfaces of ship hulls are meshed and loaded prior to the simulation, while the moving patches are dynamically discretized by a fast and robust mesh generator. The proposed method is validated for the ship- ship interaction case in the shallow water case with a flat and horizontal seabed where the mirror image technique is applicable, and satisfactory agreement is obtained. The method is further applied to simulate two interaction scenarios involving arbitrary seabed topography, and the numerical results are obtained and discussed.