Recent experimental and direct numerical simulation (DNS) studies have discovered that stably stratified boundary‐layer turbulence over a flat surface is characterized by the critical Reynolds number, ReL, based on the Obukhov turbulent length‐scale and the friction velocity, such that the transition from turbulent to laminar regime occurs at ReL ≈ 102. We have performed DNS of stably stratified flows over both flat and waved surfaces for a wide range of bulk Reynolds numbers and Richardson numbers and revealed that the same threshold, ReL = 102, holds true over waved surfaces. However, when the surface wave slope is sufficiently steep, the supercritically stratified flow involves wave‐induced, ‘pre‐turbulent’ flow patterns, most pronounced in the vicinity of the waved water surface. In the present article, we study basic properties of these motions through DNS and propose a theoretical model of their generation via secondary parametric resonance instability of two‐dimensional disturbances induced in the air‐flow by the surface waves.