Rejecting wave disturbances is critical to the safe and efficient operation of marine vehicles at sea. In this paper, we use a port-Hamiltonian representation of marine vehicles to develop a passivity-based controller for the suppression of unknown input wave disturbances using a harmonic representation while tracking a time varying reference signal. Our controller is an extension of the tracking controller of , with the addition of the input disturbance suppression using an internal model unit from . We show exponential stability for the tracking controller, and utilise Barbalat’s Lemma to show that all the signals in the input disturbance suppression controller are bounded. We illustrate our results through simulations.