The importance and role of sorting processes in dune-phase bedload transport and deposition is demonstrated with flume experiments, vibracores from the River Rhine (The Netherlands) and with sediment transport and dune data from the River Rhine. The entrainment and deposition depth of the sediment depend on dune trough levels below the average bed level and therefore on the dune height. As bedload sediment transport depends partly on grain size, it will be dependent upon the relict vertical sorting left in the bed by former discharge waves. The vertical sorting is created by sorting in grain flows on the lee side of dunes and by gravel lag formation in the dune troughs. Based on these principles, a simple reach-representative process model is developed for the prediction of bed sediment reworking, vertical sorting and deposition by dunes. The model is applied to two successive discharge waves of different magnitude, and predicts qualitatively the same vertical sorting characteristics as observed in the vibracores from the River Rhine (The Netherlands) after two successive discharge waves. The effect of the sorting on the sediment transport, and how to include this feedback in future models, is discussed.