A model linking subaqueous dune migration to the effective (grain related) shear stress is calibrated by means of flume data for bedform dimensions and migration rates. The effective shear stress is calculated on the basis of a new method assuming a near-bed layer above the mean bed level in which the current velocity accelerates towards the bedform crest. As a consequence, the effective bed shear stress corresponds to the shear stress acting directly on top of the bedform. The model operates with the critical Shields stress as a function of grain size. It predicts the deposition (volume per unit time and width) of natural packed bed material on the bedform lee side, qb_crest. The model is simple, built on a rational description of simplified sediment mechanics, and its calibration constant can be explained in accordance with estimated values of the physical constants on which it is based. Predicted values of qb_crest correlate with the measured flume data values of bedform height multiplied by bedform migration rate with R² = 0.79. The model is validated by means of independent measurements based on a flume study as well as the results from a small natural river.