Stream restoration goals include improving habitat and water quality through reconstruction of morphological features found at analogous, pristine stream reaches. Enhancing hyporheic exchange may facilitate achieving these goals. Although hyporheic exchange at restoration sites has been explored in a few previous studies, comparative studies of restored versus reference or control streams are largely absent. We hypothesized that restoration cross-vanes enhance hyporheic exchange, resulting in biogeochemical alteration of stream water chemistry in the streambed. Two streams restored using cross-vanes to control erosion and improve habitat were compared with their associated reference reaches, which provided the basis for the restoration design. Thirteen temperature profile rods with vertically stacked sensors were installed at each site for 2 weeks. Heat tracing was used to quantify vertical flux in the streambed from the diurnal temperature fluctuations in the subsurface. Stream water and bed pore waters from mini-piezometers were analysed for ion and nutrient chemistry. In general, mean vertical flux rates through the streambed were small throughout reference sites (−0.3 to 0.3 m/day) and at most locations at restored sites. Immediately adjacent to cross-vanes, vertical flux rates were larger (up to 3.5 m/day). Geochemistry of pore waters shows distinct differences in the sources for the reference and restored sites. Strong downwelling zones adjacent to cross-vanes showed high dissolved oxygen (10.75 mg/l) and geochemistry in the streambed similar to surface water. Reference sites had lower dissolved oxygen in the streambed (0.66–5.14 mg/l), and geochemical patterns suggest a mixture of discharging groundwater and surface water in the hyporheic zone. Restored sites also clearly show sulfate and nitrate reduction occurring in the streambed, which is not observed at the reference sites. The stream restoration sites studied here enhance rapid hyporheic exchange, but upwelling of groundwater has a stronger influence on streambed geochemistry at reference sites. Copyright © 2012 John Wiley & Sons, Ltd.