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There is disagreement in the literature as to whether a shear stress-based approach can be used to accurately predict sediment transport over dunes. This study aims to address this disagreement. To this end, use is made of an experiment involving the study of naturally formed, fully developed dunes produced in a laboratory flume. The bed shear stress is estimated through a combination of velocity, Reynolds stress measurements, and results of a CFD RANS rough wall model. The validity of using Bagnold’s equation to predict the bed-load rate is subsequently analyzed. In contrast to what has been previously suggested by some authors, it is found from the present experiment that the bed-load rate correlates well with the bed shear stress, and that Bagnold’s equation yields realistic values of the bed-load rate over the stoss side of the dune downstream of the reattachment point. This work also highlights the difficulties in reliably estimating the bed shear stress in complex flows. Such difficulties are overcome in this paper through a combination of flow velocity measurements and modeled results.