Gravel bed rivers have complex, porous, and irregular surfaces, characterized by a range of morphological forms. These topographical structures determine the flow structures that develop over the river bed, primarily by the shedding of vortices in the downstream wake of protruding clasts. Previous research into these flow structures has come from experimental studies, which have used either flow visualization or single-point measurements techniques. Here we present a numerical experiment where large-eddy simulation (LES) is used to study the generation, evolution, and destruction of these flow structures over a naturally water worked gravel surface. The numerical simulations reported in this paper show that there are two distinct scales of boundary influence upon the shallow flow and emphasize that the measured flow variability at any one point in a natural river will contain both locally derived and upstream-inherited flow structures, according to the range of scales of bed topography present.