The permeability heterogeneity of cross-bedded sediment increases path lengths of river-groundwater mixing (hyporheic exchange) in riverbeds and modifies the distribution of residence times. For two case studies, we numerically simulated fluid flow and solute transport through immobile bed forms composed of heterogeneous sediment and equivalent homogeneous sediment in order to clarify how cross-bedded permeability structures impact hyporheic exchange. The two permeability fields are from the cross-bedded Massillon Sandstone and modern climbing ripple deposits of the Brazos River (Texas). In both cases, permeability heterogeneity creates long hyporheic exchange paths but only slightly increases the depth of exchange relative to equivalent homogeneous sediment. In the Massillon example, permeability heterogeneity increases the proportion of long hyporheic residence times (>3 days). In the Brazos example, permeability heterogeneity increases the proportion of short residence times (<17 h). We attribute the different responses in residence time distributions to differences in permeability patterns near the sediment-water interface. The tails of residence time distributions extend for tens of years and conform to a power law in both heterogeneous and homogeneous sediment. Current–bed form interactions are responsible for the long tails, as opposed to permeability heterogeneity.