Over the last 25 y, stream ecosystem theory has expanded to include explicitly the vertical dimension of surface–groundwater linkages via the hyporheic zone and below alluvial floodplains. Hydrological exchange between the stream and hyporheic zone mediates transport of products from the biogeochemical activities within the sediments. Hot-spots of primary productivity in the surface stream often result from upwelling nutrient-rich water. Conversely, downwelling surface water supplies organic matter and dissolved O₂ to hyporheic invertebrates and microbes, enhancing hyporheic productivity. Many of the papers seminal to conceptual and empirical advances in hyporheic research have been published in J-NABS, reflecting stream benthologists' awareness of the relevance of processes and biota in the hyporheic zone. However, major research gaps remain. One is the need for further empirical data to test the predictions of several current conceptual frameworks that hypothesize conditions under which the hyporheic zone might be expected to contribute most to surface stream metabolism, especially in large rivers with shallow alluvial aquifers. A second is how to apply research findings about the functional significance of the hyporheic zone to river restoration and conservation. Many activities that restore or protect surface biota and habitats probably benefit hyporheic processes and fauna as well, but this prediction should be tested. Last, hyporheic exchange and the biogeochemical processes within the sediments occur across multiple hierarchical spatial scales, but we are yet to understand fully these interactions or to extrapolate successfully across scales. J-NABS should continue to play a significant role in publishing research on the hyporheic zone and extend the scope to include applications in river and floodplain management and restoration.