Two sets of flume experiments were conducted to examine grain size selective transport and vertical sorting in conditions with migrating bed forms and bed load transport. In the two sets of experiments we used a sediment mixture from the river Rhine and a trimodal mixture, respectively. The vertical sorting profiles showed a downward coarsening trend within the bed forms, and in some experiments an essentially immobile coarse bed layer formed underneath the migrating bed forms. Three mechanisms contribute to the formation of such a coarse bed layer: (1) the avalanching process at the lee face, (2) conditions of partial transport in which a relatively large amount of coarse material does not participate in the transport process, and (3) the winnowing of fines from the trough surface and subsurface. The experiments show that vertical sorting fluxes not only occur through net degradation or aggradation but also through the migration of bed forms and through the variability in trough elevations. This is contradictory to the way vertical sorting processes are modeled in most existing sediment continuity models for nonuniform sediment. The present study is therefore also a plea for modifying existing sediment continuity models to account for vertical sorting processes other than through net aggradation or degradation.