Model uncertainty and saturation in actuators are among some of the practical challenges in the controller design of autonomous vehicles. Incorporating adaptive control with anti-windup (AW) compensators can provide a convenient combination to counteract the challenge. In this manuscript, an adaptive control with a dynamic anti-windup compensator is proposed for an Autonomous Underwater Vehicle (AUV). Due to industrial and academic interests, the proposed method is embedded with a Proportional-Derivative-Integral (PID) controller. A modern AW technique is employed to cope with the saturation problem. Typical performance of the adaptive control system is achieved in the absence of actuator saturation. The performance is shown to degrade when the saturation has occurred. However the quality of the adaptive controller is improved when it is combined with an anti-windup compensator. Primarily six degrees of freedom (DOF) nonlinear motion equations of the vehicle are derived. Then, the proposed scheme is applied to this nonlinear model. Performance of the modified system is compared by the baseline controller. The effectiveness of the presented method in the presence of the actuator saturation, considering uncertainties, noise and disturbance is assessed and verified through simulation scenarios. (C) 2016 Elsevier B.V. All rights reserved.