This study aimed to predict ship trajectories in deep and shallow waters in real-time by properly accounting for the effects of hydrodynamic interactions on ship maneuvering. Ship maneuverability and motion control were investigated under hydrodynamic interactions arising from the effects of water depth, ship speed, and lateral distance between interacting ships on parallel courses. The Maneuvering Modeling Group (MMG) model was used, and the hydrodynamic interaction effect was estimated using an efficient three-dimensional potential-flow code that can run in real time. The influence of water depth on ship maneuverability was analyzed. The ship velocity response to the hydrodynamic interactions and maneuvering motion was simulated during the overtaking process of two ships at a range of water depths, lateral distances, and speeds. The findings suggest that, in shallow waters, changing the heading of the ship becomes more difficult, and the course deviation associated with the overtaking maneuver of two ships also increases. A conventional proportional-integral-derivative (PID) controller was employed for course-keeping. When the ratio of the water depth to ship draft was less than 2.0, the PID controller continued to perform effectively for the overtaking ship. For the overtaken ship, the effectiveness of the controller was diminished owing to the relatively low rudder effect at slow speeds.