This is the second paper in a group of three that reports the systematic measurements of wind-generated water waves in a wind tunnel experiment. Here, the structure of the boundary layer on the air side of the water–air interface was analysed and compared with the boundary layer over a smooth plane rigid wall. The contribution of the wave-induced Reynolds stress was detected through filtering the spectrum of velocity fluctuations. Wave-induced Reynolds stresses became negligible for z > 5 H rms. The intermittency factor in the boundary layer over water waves was similar to that in a boundary layer over a rigid plane wall, with several differences near the interface. Here, the presence/absence of water damps out the turbulence. The quadrant analyses revealed that ejection and sweep events were dominant and more concentrated. At small fetches, the large-amplitude negative streamwise perturbations were preferentially lifted. Turbulence energy production peaked at z/δ = 0.2 and had a distribution similar to that observed for a self-preserving boundary layer with a strong adverse gradient pressure. The quadrant analysis contribution to the energy production revealed that ejections still dominated the balance and that the production was spatially modulated in the wind direction with a couple of cells and with a minimum in the area of the free surface wave height reduction.