Hyporheic exchange is generally analyzed with the assumption of a homogeneous hyporheic zone. In reality, streambed sediments have a heterogeneous structure, and this natural heterogeneity produces spatially variable interfacial fluxes and complex hyporheic exchange patterns. To assess the basic effects of sediment structure on hyporheic exchange, we performed salt and dye injection experiments in a recirculating laboratory flume with two heterogeneous sediment beds characterized by negative-exponential correlated random hydraulic conductivity fields. Dye injections showed that the hyporheic flow structure was controlled by the spatial relationship of bed forms to high- and low-permeability regions of the streambed. As no existing model could represent these effects, we developed a new finite element model to calculate the pore water flow field resulting from the interaction of the bed form-induced boundary head distribution and the heterogeneous sediment structure. A numerical particle-tracking approach was then used to assess the resulting hyporheic exchange. The combined flow-transport model did an excellent job of predicting the complex hyporheic flow pathways in the heterogeneous bed and the net hyporheic exchange up to t ≈ 30 hours. The heterogeneous hydraulic conductivity field caused both greater spatial variability in the water flux through the bed surface and a greater average interfacial flux than would have occurred with a homogeneous bed. The layered correlation structure of the streambed produced an effective anisotropy that favored longitudinal pore water flow and caused a relatively rapid decrease of the mean pore water velocity with depth. As a result, solute penetration into the bed was confined to a more shallow region than would have occurred with a homogeneous bed. The combination of faster near-surface transport and shallower solute penetration produced a shorter mean hyporheic residence time. On the basis of the combination of experimental results and model simulations we conclude that the structural heterogeneity of streambed sediments produces more spatially limited hyporheic exchange that occurs with greater spatial variability and at a higher overall rate.