The effect of surface waves on the hydrodynamic performance of a marine current turbine (MCT) is studied using the unsteady BEM method. The calculation are found to be in a very good agreement with experimental results of a small scale MCT. It is shown that a large amplitude wave, but still a long wave can affect the time-averaged coefficient of power and also introduce non-linearity in the time response of the turbine particularly at low tip speed ratio. This can have consequence for an effective control of the turbine. Instantaneous blade loading and power spectra are given and analyzed. © 2016 IEEE.