Abstract: The hyporheic exchange plays a crucial role in maintaining fluvial ecological processes. In order to examine the influence of streambed heterogeneity on the hyporheic exchange,a surface water-groundwater coupling model is constructed for solving flow interactions over a sand dune. By generating different permeability random fields,the influences of hydrodynamic processes and streambed heterogeneity on the hyporheic exchange flux,exchange space and mean residence time are addressed. The results showed that the coupling model has good performance and it can accurately depict the flow fields near the sediment-water interface. Under homogeneous or heterogeneous scenarios,the mean exchange flux and bulk residence time via Reynolds number are representing power law relationships,and the mean exchanged depth tends to be stable after the surface flow transitions into highly turbulent conditions. Results further shown that higher heterogeneity can effectively enhance the hyporheic exchange flux and spatial exchange frequency along the sediment-water interface. However,it will restrict the exchange volume and shorten the mean residence time of flow in the hyporheic zone.