The nonhydrostatic boundary problem for an arbitrary three-dimensional domain with a seamount is considered. The problem is integrated into curvilinear boundary-fitted coordinates on a nonuniform grid. In order to identify nonhydrostatic effects the grid is condensed on the slopes of the seamount preserving a coarse resolution in the rest of the domain, where the problem is solved in the hydrostatic approximation. Calculation results for the nonhydrostatic tidal dynamics and hydrology of the Strait of Messina in the area of a seamount are presented.