The database from a Large Eddy Simulation (LES) calculation is used to investigate the dominant coherent structures in the wake of a vertical bridge abutment in a straight channel with deformed bed corresponding to equilibrium scour bathymetry. The bathymetry is obtained from an experiment conducted at the same Reynolds number. The incoming flow is fully turbulent in both experiment and simulation. Dye visualizations are used to validate the numerical predictions. It is observed the directions at which the eddies are shed in the separated shear layer change as the bed is approached. In average, the separated shear layer curved toward the lateral wall as the bed is approached. The eddies shed into the separated shear layer can entrain sediment as they are convected. This may explain one of the mechanisms responsible for the development of the scour hole in the region behind the abutment. It is also observed the formation of large scale bed forms strongly increases the complexity and three-dimensionality of the flow in the region situated between the detached shear layer and the lateral wall downstream of the abutment. In particular, a streamwise elongated submerged mount of sediment (hill) is observed to form downstream of the abutment. As a result, two streamwise-oriented vortices are identified in between the submerged hill and the lateral wall. It is found the movement of the fluid inside these vortices may be either in the flow direction or in the reverse flow direction depending on the streamwise position along their axes. The influence of these vortices on the sediment transport within the recirculation region past the abutment in the later stages of the scouring process is discussed. © 2007 ASCE.