Hyporheic zones are key compartments for the functioning of aquatic ecosystems. As dynamic and complex transition regions between rivers and aquifers, they are characterized by the simultaneous occurrence of multiple physical, biological and chemical processes. Turnover and degradation of nutrients and pollutants are among the prominent ecological services the hyporheic zone provides. We are facing a significant knowledge gap in the understanding of how hyporheic processes are linked and how they impact on each other.