The long-wave dynamics of the Lombok Strait, which is the most important link of the West Indonesian throughflow connecting the Pacific and Indian Ocean waters, was simulated and analyzed. A feature of the strait is its extremely complex relief, on which water transport creates a field of pronounced vertical velocities, which requires consideration of the nonhydrostatic component of pressure. The work presents a 3-D nonhydrostatic model in curvilinear coordinates, which is verified on a test problem. Particular attention is paid to the method of solving the 3-D elliptical solver for a nonhydrostatic problem in boundary-matched coordinates and a vertical σ level. The difference in transport through the Lombok Strait is determined by the difference in atmospheric pressure over the Pacific and Indian Oceans. Based on the results of the global simulation, the role of these factors in terms of their variability is analyzed, and the value of nonhydrostatic pressure in the dynamics of the Lombok Strait is revealed and evaluated. The vertical dynamics of the Lombok Strait are considered in detail based on hydrostatic and nonhydrostatic approaches.