This paper presents the questions of development and research of the new synthesis method of a control system for the autonomous and remotely controlled underwater robots equipped with underwater multilink manipulators. This system was designed for implementation of the widely used underwater research manipulative operations in an automatic mode. Some of them are: taking soil samples and geological rocks, determination of the composition and density of the soil with special probes and drills, taking precipitation samples with the hermetically sealed soil tubes, measurements by means of the thermistor sensors in different layers of the sedimentary soil. A control system based on the proposed method was developed. In an automatic mode, this system determines location of the bottom surface in relation to the underwater robot by means of the onboard multi-beam hydroacoustic sonar. During a robot's immersion, the developed system evaluates the complexity of the bottom relief in the working area and takes decisions on the suitability of the said relief for a trouble-free implementation of the specified manipulative tasks. Also, the proposed system determines a robot's spatial orientation and the position for the most efficient and safe manipulation operations. The algorithm for formation of the spatial trajectories of the multilink underwater manipulator's working tools was proposed. These trajectories are formed with account of the borders of the manipulator's workspace, where a sampling device can be oriented perpendicular to the bottom surface. This algorithm uses information about the continuously updated model of the bottom surface. The experimental tests of the synthesized control system were done in a deep-sea expedition for research of its operability and functioning features. The experiment results proved the efficiency and simplicity of a practical realization of the proposed system.