Abstract At river bifurcations water and sediment is divided among the downstream branches. Prediction of the sediment transport rate and division thereof at bifurcations is of utmost importance for understanding the evolution of the bifurcates for short-term management purposes and for long-term fluvial plain development. However, measured sediment transports in rivers rarely show a uniquely determined relation with hydrodynamic parameters. Commonly a hysteresis is observed of transport rate as a function of discharge or shear stress which cannot be explained with the standard sediment transport predictor approach. The aim of this paper is to investigate the causes of hysteresis at a bifurcation of the lower Rhine river, a meandering river with stable banks, large dunes during flood, and poorly sorted bed sediment. The hydrodynamics and bed sediment transport were measured in detail during a discharge wave with a recurrence interval larger than 10 years. Surprisingly, the hysteresis in bedload against discharge was in the opposite direction upstream and downstream of the bifurcation. The upstream clockwise hysteresis is caused by the lagging development of dunes during the flood. The counter-clockwise hysteresis downstream of the bifurcation is caused by a combination of processes in addition to dune lagging, namely 1) formation of a scour zone upstream of the bifurcation, causing a migrating fine sediment wave, and 2) vertical bed sorting of the bed sediment by dunes with avalanching lee-sides, together leading to surface-sediment fining and increased transport during and after the flood. These findings lead to challenges for future morphological models, particularly for bifurcations, which will have to deal with varying discharge, sediment sorting in the channel bed, lagging dunes and related hydraulic roughness.