The effect of hydrodynamic performance of the wave energy converter (WEC)–rotor based on linear potential flow theory due to nonlinear viscous damping was investigated. Free decay tests were conducted using computational fluid dynamics (CFD) to obtain the viscous damping moment. The commonly used procedure for obtaining the damping moment is based on peak amplitudes which normally require a long time history records. Such long free decay records may not be possible in nodding WEC rotor due high damping. The energy method proposed by Bass and Haddara requires only the short and full range of the recorded data. This method provides sufficiently good results when the bodies have high damping. The method equates the rate of change of the total energy of a body undergoing free rolling/pitching to the rate of energy dissipated by the damping. The present study adopts a similar methodology for estimating the linear and linear plus quadratic damping. To incorporate the nonlinear viscous damping moment in the linear equation of motion, an equivalent linearization concept is used without neglecting the nonlinear damping effects. The hydrodynamic coefficients obtained from the linear potential flow theory, nonlinear viscous damping moment from the energy method and estimated PTO damping are used to solve the equation of motion of the WEC rotor. The estimated pitch free decay data shows good agreement with the simulated CFD results when compared to the linear viscous damping moment and better agreement is obtained with linear plus quadratic viscous damping moment. The regular and irregular wave analyses show that a considerable effect on the hydrodynamic performance of the WEC rotor is observed when the linear and linear plus quadratic viscous damping are included.