Turbulent flows moving over a gravel bed develop large-scale, macroturbulent flow structures that are initiated at anchor clasts in the bed and grow and dissipate as they move upward through the flow depth. This paper extends previous research in which we investigated the influence of the Reynolds number on coherent flow structures generated over a gravel bed by assessing the importance of effective bed roughness. Here, we report on flume experiments in which flows over beds of decreasing surface roughness have been quantified through the application of digital particle imaging velocimetry, which allows study of the downstream and vertical components of velocity over the entire flow field. These results indicate that as the effective roughness increases (1) the visual distinctiveness of the coherent flow structures becomes more defined throughout the flow depth, (2) the upstream angle of slope of the coherent flow structure increases, and (3) the reduction in streamwise flow velocity and turbulence intensity toward the upstream side of the structure becomes greater. Applying standard scaling laws, these structures appear shear-generated and form through a combination of both wake flapping and the reattachment of localized shear layers associated with flow separation around individual topographic protrusions. As the effective protrusion decreases, the scale of these coherent flow structures also decreases.