We present results from open-channel, Euler–Lagrange (EL) simulations of turbulent flow over an erodible particle bed at a shear Reynolds number of$Re_{\tau }=180$. Upon space and time averaging, our simulations correctly reproduce the Wong & Parker (ASCE J. Hydraul. Engng, vol. 132, issue 11, 2006, pp. 1159–1168) bedload transport relation (WP). However, local and instantaneous sediment flux shows orders of magnitude scatter around the WP prediction. Visualization of the vortical structures using swirling strength shows the existence of bed-penetrating Kelvin–Helmholtz (KH) vortex packets, which coupled with particle inertia are primarily responsible for the large scatter. The results also show that Euler–Euler (EE) simulations, where the individual sediment grains are not distinguished, are still able to reliably capture the turbulent shear stress variation, however, they do not capture the wide distribution of sediment flux indicative of saltating transport. The KH vortices induce non-zero streamwise and bed-normal velocities at the upper surface of the bed, which must be considered in EE simulations.