In this paper, a novel robust trajectory tracking control law is proposed for marine surface vessels with uncertain disturbances and input saturations using a tan-type barrier Lyapunov function and a backstepping technique. The low-frequency disturbances in kinetics from wind and waves are estimated by a nonlinear finite-time disturbance observer (FTDO). An adaptive estimation law is employed to estimate the unknown time-varying current velocities. A Gaussian error function-based continuous differentiable asymmetric saturation model is employed to handle the effect of nonsmooth asymmetric saturation nonlinearity using a backstepping technique, and auxiliary dynamic systems are used to compensate for the input saturation constraints on the actuators. Lyapunov stability analysis proves that all the signals of the closed-loop systems are guaranteed to be semi-globally uniformly ultimately bounded, and the tracking errors can converge to a small neighborhood of the origin by appropriately selecting the control parameters. Simulations and comparison results are presented to verify the effectiveness of the proposed method.