Abstract Recent experiments in the river Seine have revealed the presence of persistent large rolls. This finding has motivated the present numerical study of a turbulent open channel flow. Our pseudo-spectral direct numerical simulations are aimed at understanding how the shear at the surface, for instance produced by an external wind, can change vortical structures in the bulk. Simulations are run at a Reynolds number in the range $$[5\times 10^3\div 10^4]$$ [ 5 × 10 3 ÷ 10 4 ] , in line with similar laboratory experiments. We investigate how flow structures located near the bottom wall, near the surface or inside the bulk are modified by a surface shear. Statistical signatures are extracted through Fourier analysis of the simulated fields, and typical wavelengths of vortices or streaks are computed. Moreover, instantaneous fields are used to show the existence of upwelling and downwelling motions. These motions can be hindered by the presence of a large enough surface shear. This condition turns out to be necessary for the existence of streaks at the surface as well. Our investigation clarifies the dynamics of vortices in an open channel flow at moderate Reynolds number, indicating that unsteady vortex structures are indeed present, but the existence of long coherent rolls cannot be accounted for by the sole presence of shear at the surface. Numerical studies with a much longer domain and possibly at higher Reynolds numbers are needed to provide a firm answer to the question.