Highly uncertain and complex structures of marine vehicles render the control problem a challenging task. Moreover, the problem becomes much more challenging when the system is exposed to environmental disturbances. This thesis tackles this control problem with an adaptive robust control algorithm which is fused with a periodic disturbance estimation method. The periodic disturbance estimation method inspired from a Fourier series expansion technique is applied for compensation of environmental forces. In the first part of the thesis, an adaptive full state feedback backstepping controller which is supported with the periodic disturbance estimation method is applied. Stability of the closed–loop system and the convergence of the tracking error are established via Lyapunov based methods. Simulation studies are provided to support the theoretical results and to demonstrate the effectiveness of the proposed method. In the second part of the thesis, a nonlinear model free observer based adaptive output feedback controller in conjunction with the periodic disturbance estimator is designed. Lyapunov based arguments have been utilized to prove the stability of the closed– loop system, and the convergence of the tracking and observer errors under the closed– loop operation. Performance and viability of the proposed method are demonstrated via numerical simulations.