Local scour around elongated in-stream structures (e.g., high–aspect ratio rectangular bridge piers) is mainly driven by the interactions between the erodible bed and the large-scale coherent structures generated by the presence of the flow obstruction. The present investigation uses eddy-resolving numerical simulations to study the mean flow and turbulence structure around a high–aspect ratio rectangular cylinder placed in a flat bed channel. Simulations are conducted for three angles of attack (α = 0°, 15°, and 30°) at a channel Reynolds number of 2.4 × 105. This paper focuses on the dynamics of the large-scale coherent structures forming around the rectangular cylinder and their role in controlling sediment entrainment at conditions corresponding to the start of the scour process. Simulation results show that most of the sediment is entrained from the bed by the eddies shed inside the separated shear layers (SSLs), by the legs of the necklace vortices, and by the strongly accelerated flow on the outer side of the SSLs. For α = 0° and 15°, the horseshoe vortex (HV) system plays a relatively minor role in the entrainment of sediment in front of the cylinder, and the passage of the wake vortices (rollers) results in a small amplification of the bed friction velocity. In contrast, for α = 30°, the unsteady dynamics of the main necklace vortices part of the HV system and of the roller vortices results in a significant amplification of the instantaneous bed friction velocity. The mean flux of sediment entrained from the bed calculated on the basis of the mean flow field is found to underestimate by 2–3 times the same quantity when estimated more correctly on the basis of the instantaneous flow fields. The primary reason for this underestimation is sediment entrainment in regions where the mean flow bed friction velocity is smaller than the critical value for entrainment. Quantitative information on the extent of the regions of high values of the bed friction velocity and its standard deviation and on the sediment entrainment flux as a function of the angle of attack is essential to guide scour protection measures around the in-stream noncircular obstructions.