The object of this researching is the process of maneuvering a sea-based vehicle under compressed conditions, which requires one hundred percent reserve of thrusters (THRs) of various modifications and locations. The main problem is the provision of energy-efficient control over the ship's motion at low speed in the horizontal plane using a high-level predictive controller. The hierarchy of the motion control system (MCS) is usually divided into several levels with the help of a high-level motion controller and the THR motor control distribution algorithm. This allows for a modular software structure where a high-level controller (HLC) can be designed without using comprehensive information about the THR motors. However, for a certain reference of THR configurations, such a decoupling can lead to reduced control performance due to the limitations of HLC regarding the physical constraints of the vessel and the behavior of MCS. The main results of the researching are methods to improve control performance using a nonlinear model predictive control (MPC) as a basis for the designed motion controllers due to its optimized solution and ability to consider constraints. A decoupled system was implemented for two simple motor tasks showing dissociation problems. The shortcomings were eliminated through the development of a nonlinear MPC controller, which combines the motion controller and the distribution of control over THR motors. To preserve the discrete modularity of the control system and achieve adequate performance, a nonlinear MPC controller with time-varying constraints was designed. This has made it possible to take into account the current limitations of the THR control system, increase the accuracy of control, and reduce the response time of the system by 10 %.