The present study investigates the flow physics and the role played by the main coherent structures in the scouring processes around a vertical spur dike in a straight channel at conditions corresponding to the start (flat bed) of the scouring process. Large eddy simulation (LES) is performed at a relatively low channel Reynolds number (Re = 18,000), in the range where most flume studies with clear water scour conditions are conducted. Similar to these studies, the incoming flow is fully turbulent and contains realistic turbulence fluctuations. Visualization experiments are conducted to better understand the nature of the interactions between the dominant coherent structures playing a role in the erosion process. It is found that the structure of the horseshoe vortex (HV) system at the base of the spur dike changes considerably in time and in vertical sections perpendicular to the trajectory defined by the axis of the main necklace vortex. However, its intensity is the largest at vertical sections situated around the tip of the spur dike. It is in this region that the core of the main necklace vortex oscillates aperiodically between two preferred modes. In one of them (zero-flow mode), the necklace vortex is closer to the spur dike and more compact, and the near-bed jet flow beneath it is weak. In the other one (back-flow mode), a strong near-bed jet flow convects the primary necklace vortex away from the spur dike, and its core is more elongated and less compact. This explains the large amplification (by about 1 order of magnitude compared to the surrounding turbulent flow) of the turbulent kinetic energy and pressure fluctuations inside the HV system in the region situated around the tip of the spur dike and the double-peak distribution of the turbulent kinetic energy. Past the spur dike, in the legs of the necklace vortex, the intensity of the bimodal oscillations decreases such that they are not observed in spanwise sections situated at more than one channel depth behind the spur dike. It is found that the legs of the horseshoe vortices can interact, at times, with the vortex tubes shed in the detached shear layer (DSL) and with the tip of the spur dike. These events typically result in a significant change in the coherence of the HV system. The largest bed shear stress values in the mean flow are present in the strong acceleration region near the tip of the spur dike, but high bed shear stress values are also observed beneath the upstream part of the DSL. The bed shear stress fluctuations around the local mean values can be very high, especially in the region situated beneath the upstream part of the DSL. At random times, some of the vortices shed in the DSL merge or interact with eddies from the recirculation region. This leads to an increase in their strength and to a large increase of the bed shear stress along their path.