This study presents a comprehensive analysis of the second-order perturbation theory applied to the Navier–Stokes equations governing free surface flows. We focus on gravity–capillary surface waves in incompressible viscous fluids of finite depth over a flat bottom. The amplitude of these waves is regarded as the perturbation parameter. A systematic derivation of a nonlinear-surface-wave equation is presented that fully takes into account dispersion, while nonlinearity is included in the leading order. However, the presence of infinitely many over-damped modes has been neglected and only the two least-damped modes are considered. The new surface-wave equation is formulated in wave-number space rather than real space and nonlinear terms contain convolutions making the equation an integro-differential equation. Some preliminary numerical results are compared with computational-modelling data obtained via open source CFD software OpenFOAM.