This paper deals with the development of the Guidance Navigation and Control (GNC) system of the Autonomous Underwater Vehicle (AUV) used for acoustic surveys in the WiMUST projects. By exploiting the fact that the vehicle hull has a modular structure, a specific payload module was realized containing a single board computer, two acoustic modems, the electronic boards for signal conditioning and data storage of seismic data, and the mechanical interface for the streamer, the array of hydrophones that constitutes the main mission payload. Then, by using the Robot Operating System (ROS) the mission control system was implemented in the single board computer inside the additional payload segment. Motion control for the AUV was realized designing controllers for surge speed, heading and depth. Design of the depth controller represented one of the major challenges mainly because towing the streamer heavily affects the vehicle dynamics when underwater. Thus, a specific fuzzy-PID control system was implemented and tested. This one, together with the surge speed and the heading controller are discussed in this paper. Finally, selected experimental results from sea trials are discussed to prove the effectiveness of the presented GNC system.