Large eddy simulation (LES) is used to investigate the flow around a vertical spur dike in a straight channel with equilibrium scour bathymetry and the scour mechanisms in the later stages of the erosion deposition process. The equilibrium bathymetry is obtained from an experiment conducted at the same relatively low channel Reynolds number (Re = 18,000). Flow visualizations are used to complement the information obtained from the numerical simulation. The present investigation demonstrates that large-scale bimodal oscillations of the primary necklace vortex are the main reason for the amplification of the turbulence inside the scour hole. The nature of these oscillations is similar to the one observed in the horseshoe vortex (HV) system forming in the flow past bluff bodies (e. g., spur dikes) mounted on flat surfaces. The presence of the scour hole stabilizes the HV system compared to the case when the bed is flat. It is observed that random ejection of vorticity patches from the legs of the necklace structures takes place at random times. The axis of the vorticity patch remains approximately parallel to the bed. These patches of high vorticity move predominantly against the mean slope of the scour hole and can cause sediment entrainment as they are convected over the bed before they dissipate. This mechanism explains, at least partially, the lateral growth of the scour hole in the later stages of the scouring process. As a result of merging phenomena, some of the eddies convected in the detached shear layer (DSL) can also induce large local value of the bed shear stress. The variation in the mean shape of the DSL as the bed is approached is another phenomenon observed in the current study. Close to the bed, at some time instances the DSL tends to curve toward the back of the spur dike, whereas at higher elevations the DSL regains the shape typically encountered in the flow over a surface-mounted wall of infinite width. In the near-bed region, the DSL is observed to oscillate between these two extreme positions. This explains how the scour hole grows in the region situated just behind the spur dike and how the entrained sediment is then transported in the deposition area behind the spur dike. The role of the two streamwise-oriented vortices, present in between the elongated submerged deposition hill and the channel sidewall, in the sediment transport processes inside the wake region is discussed. The predicted mean bed shear stress distribution around the spur dike is consistent with the equilibrium conditions present in the experiment.