1. The hyporheic zone below the channel and banks of many rivers where surface water and ground water exchanges plays a crucial functional role in the biogeochemical transformation of water, mediated by active microbial biofilms. This zone also harbours assemblages of invertebrates that graze biofilms, contribute to secondary production, and can alter the porosity of the hyporheic zone through their movement or burrowing activities.
2. Many human activities cause interstitial sedimentation or disrupt surface–groundwater hydrological linkages, impacting upon ecological processes in the hyporheic zone. However, strategies for river rehabilitation seldom explicitly consider the hyporheic zone or seek to restore lost vertical linkages with groundwater. Instead, restoration goals target surface, riparian or floodplain features even though current river ecosystem theory emphasises the three dimensions of hydrological connectivity. To guide effective, holistic river restoration, scientists and managers therefore need information on the mechanisms by which energy and material are transferred in the hyporheic zone and which ecosystem services are thus provided.
3. Other gaps in our understanding of hyporheic zone rehabilitation include recruitment processes of the hyporheos and the relative importance of groups of hyporheic invertebrates in rivers differing in substratum size, disturbance frequency and groundwater linkages. Carefully designed experiments that assess responses to hyporheic rehabilitation strategies will provide valuable data at varying scales (e.g. distribution of hyporheic habitat types at the reach scale) for management as well as providing insights into the mechanisms controlling hyporheic invertebrate assemblages and ecological processes. Fully successful river rehabilitation must include restoration of vertical linkages between the river and its shallow groundwater aquifers.