The process which leads to the appearance of three-dimensional vortex structures in the oscillatory flow over two-dimensional ripples is investigated by means of direct numerical simulations of Navier–Stokes and continuity equations. The results by Hara & Mei (1990a), who considered ripples of small amplitude or weak fluid oscillations, are extended by considering ripples of larger amplitude and stronger flows respectively. Nonlinear effects, which were ignored in the analysis carried out by Hara & Mei (1990a), are found either to have a destabilizing effect or to delay the appearance of three-dimensional flow patterns, depending on the values of the parameters. An attempt to simulate the flow over actual ripples is made for moderate values of the Reynolds number. In this case the instability of the basic two-dimensional flow with respect to transverse perturbations makes the free shear layer generated by boundary layer separation become wavy as it leaves the ripple crest. Then the amplitude of the waviness increases and eventually complex three-dimensional vortex structures appear which are ejected in the irrotational region. Sometimes the formation of mushroom vortices is observed.