This article considers an approach to synthesizing a multilevel system to control movements of a multilink manipulator (MM) mounted on an unmanned underwater vehicle (UUV) for performing autonomous manipulative operations in the mode of dynamic positioning over various objects on the seafloor. The system is based on an upgraded method that, using point clouds received from the machine vision systems (MVS), provides high-accuracy determination of the shape and location of the work object relative to UUV. The preset trajectories of the MM working tool are overlaid on the identified surface of the object, with possible silting, fouling or deformation of the latter taken into account. To execute the programmed trajectories with the MM working tool, the following methods have been implemented in software: stabilization of UUV in hovering mode near the object, high-precision control of working tool’s movements, and also corrections of its trajectory taking into account UUV’s displacements relative to the object. The synthesized system has been developed in the C++ programming language. The operation of the system has been numerically simulated using a model of UUV with MM, as well as models of the environment and the target object, in the Matlab/Simulink and V-REP software packages. The results of the study show a high efficiency of the system both in processing sensor information and in providing the dynamic control of movements of an UUV with a MM.