This paper describes a model developed to predict the general behavior of large vessels under energetic tsunami conditions using established regional-scale tsunami models. The methodology is based on a two-way coupled approach to account for the interaction between vessels and flow, which becomes increasingly important in restricted waters. A shallow water hydrodynamic solver is modified to include vessels as horizontal pressure distributions, and friction coefficients are adjusted accordingly at the locations of vessels to account for the effects of skin friction. Adequacy of these modifications are then tested against a benchmark case designed in OpenFOAM®, and comparisons demonstrate the modified shallow water solver's ability to provide a reasonable realization for energetic flow passing a floating object. A vessel transport model coupled with the hydrodynamic solver is based on the linear equations of ship motion with three degrees of freedom (surge, sway and the yaw). Finally, the model is equipped with a collision solver founded on the concept of the conservation of momentum and impulse. Results from two large scale applications of the developed tool are presented. These analyses revealed that the flow in and around the ports is indeed strongly affected by the presence of vessels. Also, it is observed that the model can approximate the ship's behavior, but at the same time the model results are very sensitive to the initial choice of the input parameters due to the chaotic nature of the process.