River restoration is a multi-billion-dollar business, yet it is unclear whether benthic community health, which is routinely monitored, can be used as a proxy for the health of the hyporheos. Applying a Before-After-Control-Impact approach to a UK case study, we compared the effects of removing an impoundment on the hyporheos with effects on the benthos. We compared invertebrate biological traits that we expected to respond to the restoration. We constructed sample-size based diversity curves and determined β-diversity between compartments and reaches. Two years post-restoration, hyporheic taxon richness was significantly lower in the restored reach compared to the control. However, three years post-restoration taxon richness was significantly higher in the impact reach. The composition of the control and impact reach hyporheos was most dissimilar at the first sampling time point post-restoration and at this time there was a universal decrease in the relative abundance of burrowing organisms respiring through gills. We did not detect a signal of restoration on benthic assemblage diversity and composition, perhaps because reach-scale restorations can be overwhelmed by catchment-scale disturbances. Thus, the hyporheos and the benthos responded differently to restoration. Given the importance of the hyporheic zone in the provision of ecosystem function and services, it is clear that it should be included in future monitoring protocols that aim to assess river restoration success.