In this paper, an intelligent navigation system for an unmanned underwater vehicle powered by renewable energy and designed for shadow water inspection in missions of a long duration is proposed. The system is composed of an underwater vehicle, which tows a surface vehicle. The surface vehicle is a small boat with photovoltaic panels, a methanol fuel cell and communication equipment, which provides energy and communication to the underwater vehicle. The underwater vehicle has sensors to monitor the underwater environment such as sidescan sonar and a video camera in a flexible configuration and sensors to measure the physical and chemical parameters of water quality on predefined paths for long distances. The underwater vehicle implements a biologically inspired neural architecture for autonomous intelligent navigation. Navigation is carried out by integrating a kinematic adaptive neuro-controller for trajectory tracking and an obstacle avoidance adaptive neuro- controller. The autonomous underwater vehicle is capable of operating during long periods of observation and monitoring. This autonomous vehicle is a good tool for observing large areas of sea, since it operates for long periods of time due to the contribution of renewable energy. It correlates all sensor data for time and geodetic position. This vehicle has been used for monitoring the Mar Menor lagoon.