In gravel bed rivers, the microtopography of the bed exerts a significant effect on the generation of turbulent flow structures. Although field and laboratory measurements have indicated that flows over gravel beds contain coherent macroturbulent flow structures, the origin of these phenomena, and their relationship to the ensemble of individual roughness elements forming the bed, is not quantitatively well understood. Here we report upon a flume experiment in which flow over a gravel surface is 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. The results indicate that as the Reynolds number increases (1) the visual distinctiveness of the coherent flow structures becomes more defined, (2) the upstream slope of the structures increases, and (3) the turbulence intensity of the structures increases. Analysis of the mean velocity components, the turbulence intensity, and the flow structure using quadrant analysis demonstrates that these large‐scale turbulent structures originate from flow interactions with the bed topography. Detection of the dominant temporal length scales through wavelet analysis enables calculation of mean separation zone lengths associated with the gravel roughness through standard scaling laws. The calculated separation zone lengths demonstrate that wake flapping is a dominant mechanism in the production of large‐scale coherent flow structures in gravel bed rivers. Thus, we show that coherent flow structures over gravels owe their origin to bed‐generated turbulence and that large‐scale outer layer structures are the result of flow‐topography interactions in the near‐bed region associated with wake flapping.