In many rivers, the hyporheic zone regulates fundamental ecosystem processes at reach to catchment scales, influencing surface water quality and primary production. Over the last twenty years, hyporheic research has advanced from primarily description to include prediction and manipulation, particularly in the emerging field of hyporheic restoration. Nonetheless, gaps remain in our understanding of hyporheic ecology. Ambiguities include tests of the hyporheic refuge hypothesis, predictive models of microbial activity and composition in relation to hydrological exchange, hyporheic food-web structure, and regional differences in ecosystem services performed by the hyporheic zone. Research priorities identified twenty years ago in scale-associated heterogeneity, hierarchical organisation of hyporheic systems, and hydrologically driven emergent properties of hyporheic exchange remain, especially the need to understand the cumulative effects of sequential hyporheic zones at sub-catchment and catchment-scales. We suggest future hyporheic aspirations and some ways to address them, recognizing recent technological advances that enable us to tackle these large-scale research priorities.