Motivated by the need to gain fundamental insights into the mechanisms of bed-load sediment transport in turbulent junction flows, we carry out a computational study of Lagrangian dynamics of inertial particles initially placed on the bed upstream of a surface-mounted circular cylinder in a rectangular open channel (Dargahi, J. Hydraul. Engng, vol. 116, 1990, pp. 1197–1214). The flow field at Re = 39000 is simulated using the detached eddy simulation (DES) approach (Spalart et al., In Advances in DNS/LES, ed. C. Liu & Z. Liu, 1997, Greyden), which has already been shown to accurately resolve most of the turbulent stresses produced by the low-frequency, bimodal fluctuations of the turbulent horseshoe vortex (Paik et al., J. Hydraul. Engng, vol. 131, 1990, pp. 441–456; Escauriaza & Sotiropoulos, Flow Turbul. Combust., 2010, in press). The trajectory and momentum equations for the sediment particles are integrated numerically simultaneously with the flow governing equations assuming one-way coupling and neglecting particle-to-particle interactions (dilute flow) but taking into account bed–particle interactions and the effects of the instantaneous hydrodynamic forces induced by the resolved fluctuations of the coherent vortical structures. The computed results show that, in accordance with the simulated clear-water scour condition (i.e. the magnitude of the particle stresses is near the threshold of motion), the transport of sediment grains is highly intermittent and exhibits essentially all the characteristics of bed-load sediment transport observed in laboratory and field experiments. Groups of sediment grains are dislodged from the bed simultaneously in seemingly random bursting events and begin to move, saltating or sliding along the bed. Furthermore, particles that are not entrained into the bed-load layer are found to form streaks aligned with near-wall vortices around the cylinder. The global transport of particles is studied by performing a statistical analysis of the bed-load flux to reveal scale-invariance of the process and multifractality of particle transport as the overall effect of the coherent structures of the flow. A major finding of this work is that a relatively simple Lagrangian model coupled with a coherent-structure resolving simulation of the turbulent flow is able to reproduce the sediment dynamics observed in multiple experiments performed under similar conditions, and provide fundamental information on the initiation of motion and the multifractal nature of bed-load transport processes. The results also motivate the development of new Eulerian bed-load transport models that consider unsteady conditions and incorporate the intermittency of the unresolved scales of sediment motion.