Abstract The branches of the River Rhine in the Netherlands, characterized by a sand–gravel bed in the upstream part and a sand bed in the downstream part of the river system, show migrating dunes, especially during floods. In the last 20 years, these dunes have been studied extensively. High-resolution echo-sounding measurements of these dunes, made with single and multibeam equipment, were analysed for three different sections of the Rhine river system during several floods. This analysis was done to quantify the growth, decay and migration rates of the dunes during floods. In addition, the migrating dunes were used to calculate bedload transport rates with dune tracking. The results of dune growth and decay and migration rate are shown to be very different for the various sections during the various floods, and these differences are related to differences in grain size of the bed and to differences in the distribution of discharge over the main channel and the floodplain. The relations are used to show that the growth and migration rate of dunes, and the calculated bedload transport rates during the rising stage of a flood wave can be predicted from the mobility of the bed material with simple power relations.