Dune bedforms and salt-wedge intrusions are common features in many estuaries with sand beds, and yet little is known about the interactions between the two. Flow visualization with an echosounder and velocity measurements with an acoustic Doppler current profiler over areas of flat-bed and sand dunes in the highly-stratified Fraser River estuary, Canada, were used to examine the effect of dunes on interfacial mixing. As the salt-wedge migrates upstream over the flat-bed, mixing is restricted to the lower portion of the water column. However, as the salt-wedge migrates into the dune field from the flat bed, there is a dramatic change in the flow, and large internal in-phase waves develop over each of the larger dunes, with water from the salt-wedge reaching the surface of the estuary. The friction Richardson number shows that bed friction is more important in interfacial mixing over the dunes than over the flat-bed, and a plot of internal Froude Number versus obstacle (dune) height shows that the salt-wedge flow over the dunes is mainly supercritical. Such bedforms can be expected to cause similar effects in interfacial mixing in other estuaries and sediment-laden density currents, and may thus be influential in fluid mixing and sediment transport. Copyright © 2010 John Wiley & Sons, Ltd.