Complex and highly coupled dynamics, time-variance, unpredictable disturbances and lack of knowledge of hydrodynamic parameters, complicate the control of underwater vehicles. This paper deals with the adaptive disturbance observer design for the robust trajectory tracking problem for underwater vehicles in presence of unknown external disturbances and parametric uncertainties. First, the dynamics of the vehicle is transformed into the so-called regular form. Then, based on the Extended State Observer technique and High Order Sliding Modes Control, a disturbance observer is proposed. Furthermore, the gains of the observer are automatically adjusted by the introduction of an adaption law. The stability of the whole controller/observer scheme is proven using Lyapunov's arguments. The adaptive disturbance observer aims to improve the Backstepping and nonlinear PD controllers. Real-Time experiments demonstrate the effectiveness of the proposed algorithm for the trajectory tracking task under several scenarios.