Abstract Data are presented of experiments with turbulent open channel flow over rough surfaces and large relative submergence, which are conducted in two series with different geometric boundary conditions. During the experiments an oscillating fluid motion in the uppermost filter layer is visualised by the injection of a tracer dye. It is shown that this oscillating fluid motion is driven by highly unsteady pressure gradients and contributes to in- and outflow at the interface between surface and subsurface flow, but its intensity decays rapidly with increasing filter depth. About 90% of the high frequency pressure fluctuations measured at the surface of the filter layer are damped at a filter depth of about 4–5 times the average gravel size of the surface of the bed. It is assumed that the considered high frequency oscillations originate from turbulent pressure fluctuations in the near bed layer. The exponential function that fits the decay of turbulent pressure fluctuations implies a length scale of about 12 times the geometric roughness height as dominant wavelength of a turbulent structure, which imposes a pressure fluctuation on a riverbed. The presented results reveal that micro scale advective transport between surface and subsurface flow occurs separate from diffusive effects and should be considered for the transfer of solutes like dissolved oxygen from fresh to subsurface water and its respiration in the uppermost sediment of aquatic beds.