This work considers the re-design of an autonomous underwater vehicle (AUV) in which an innovative, neurobiological inspired sensorization control system is being implemented. Hardware architecture and sensorization control software are being developed to allow autonomous navigation procedures for submarine vehicles. After the refurbishment of the vehicle and the update of its control system, the ROV is able to load CTD sensors, chlorophyll, turbidity, optical dissolved oxygen (YSI V6600 sonde) and nitrate analyzer (SUNA) together with ADCP, side scan sonar and video camera, in a flexible configuration to provide a water quality monitoring platform with mapping capabilitiesi.