Instabilities of deep-water wave trains subject to initially small perturbations (which then grow exponentially) can lead to extreme waves in offshore regions. The present study focuses on the two-dimensional Benjamin–Feir (or modulational) instability and the three-dimensional crescent (or horseshoe) waves, also known as Class I and Class II instabilities, respectively. Numerical studies on Class I and Class II wave instabilities to date have been mostly limited to models founded on potential flow theory; thus, they could only properly investigate the process from initial growth of the perturbations to the initial breaking point. The present study conducts numerical simulations to investigate the generation and development of wave instabilities involving the wave breaking process. A computational fluid dynamics (CFD) model solving Reynolds-averaged Navier–Stokes (RANS) equations coupled with a turbulence closure model in terms of the Reynolds stress model is applied. Wave form evolutions, Fourier amplitudes, and the turbulence beneath the broken waves are investigated.