Trains of secondary bedforms, superimposed on primary dunes, have been observed in rivers worldwide. To date, it has remained unclear how these secondary bedforms affect the sediment transport dynamics in a fluvial system. In this study, a field campaign was conducted to acquire a data set with a high spatial and temporal resolution, enabling to track secondary bedform migration. Results show that two distinct scales of bedforms are actively migrating. In parts of the study area, superimposed bedforms fully dissipate at the lee slope of the underlying primary dune, suggesting that the secondary bedforms contribute to the migration of the primary dune. In other parts, however, superimposed bedforms persist on the lee slope and in the trough of the primary dune. The steepness of the primary lee slope seems to control this. We calculated the sediment transport rates associated with both primary and secondary bedform migration, based on dune tracking. The sediment transport associated with secondary bedform migration is of the same order of magnitude, and even exceeds the transport associated with primary dune migration. This implies that secondary bedforms play a crucial role in the transport of bedload sediment, and cannot be ignored in the quantification of sediment transport based on dune tracking.