Nonhydrostatic boundary-value problem is considered in the 3-D domain represented a strait with mountain relief. The equations are integrated in boundary-fitted coordinates or irregular grid. Numerical method uses the operator splitting with inversion of the 3-D Laplace-Beltrami operator at the each time step and consequent determination of the velocity field. Method is applied for simulation nonhydrostatic dynamics in the Strait of Bab-el-Mandab (Red Sea) in the winter season.