In river, estuarine and coastal environments, the diffusive boundary layer (DBL) model is typically employed to describe the solute fluxes between the sediments and the overlying water column. This model assumes that vertical diffusion at the sediment-water interface occurs at molecular rates. Recent studies, however, show that measured fluxes can be several orders of magnitude larger than can be explained by molecular diffusion alone. Here, we investigate one mechanism for enhanced interfacial fluxes, namely the generation of coherent structures at the sediment-water interface. To demonstrate the existence of coherent structures at the interface, and their influence on interfacial exchange, the experimental methodology used is a combination of Particle Tracking Velocimetry (PTV) and Refractive Index Matching (RIM). This allows simultaneous acquisition of instantaneous flow fields both above and below the sediment-water interface. The results demonstrate a strong dependence of the flow characteristics on the permeability Reynolds number Re_K = √KU/ν: for low Re_K the flow resembles an impermeable boundary layer, while for high Re_K the flow resembles a mixing-layer-type flow where the DBL model is no longer applicable. In the high-Re_K case swirl of the instantaneous velocity field shows the existence of coherent structures at the interface and, from observations of the trajectories of the tracer particles, these coherent structures extend well into the interstitial fluid in the sediment bed. These coherent structures become more pronounced with increasing Re_K.