The interface between groundwater and surface water within riverine/riparian ecosystems—the hyporheic zone (HZ)—is experiencing a rapid growth of research interest from a range of scientific disciplines, often with different perspectives. The majority of the multi-disciplinary research aims to elucidate HZ process dynamics and their importance for surface water and groundwater ecohydrology and biogeochemical cycling. This paper presents a critical inter-disciplinary review of recent advances of research centred on the HZ and highlights the current state of knowledge regarding hydrological, biogeochemical and ecohydrological process understanding. The spatial and temporal variability of surface water and groundwater exchange (hyporheic exchange flows), biogeochemical cycling and heat exchange (thermal regime) are considered in relation to both experimental measurements and modelling of these phenomena. We explore how this knowledge has helped to increase our understanding of HZ ecohydrology, and particularly its invertebrate community, the processing of organic matter, trophic cascading and ecosystem engineering by macrophytes and other organisms across a range of spatial and temporal scales. In addition to providing a detailed review of HZ functions, we present an inter-disciplinary perspective on how to advance and integrate HZ process understanding across traditional discipline boundaries. We therefore attempt to highlight knowledge gaps and research needs within the individual disciplines and demonstrate how innovations and advances in research, made within traditional subject-specific boundaries (e.g. hydrology, biochemistry and ecology), can be used to enhance inter-disciplinary scientific progress by cross-system comparisons and fostering of greater dialogue between scientific disciplines. Copyright © 2010 John Wiley & Sons, Ltd.