The development and research of the new synthesis method of the control system for an autonomous underwater vehicle (AUV) with a multilink manipulator is described in the paper. This system provides an automatic soil sampling and the taking of geological samples of a sea bottom surface. In automatic mode, the developed system defines the location of a bottom surface relative to the AUV by means of the onboard multibeam Doppler lag. During the vehicle immersion, the system evaluates the complexity of the bottom relief in the working area and makes decision on the suitability of the said relief for the trouble-free implementation of the specified manipulative tasks. Also, the proposed system realises the formation algorithm for spatial trajectories of the multilink underwater manipulator's working tool and defines the AUV spatial orientation and position at which the performing of manipulation operations occurs most efficiently and safely.