Interest in groundwater (GW)-surface water (SW) interactions has grown steadily over the last two decades. New regulations such as the EU Water Framework Directive (WFD) now call for a sustainable management of coupled ground- and surface water resources and linked ecosystems. Embracing this mandate requires new interdisciplinary research on GW-SW systems that addresses the linkages between hydrology, biogeochemistry and ecology at nested scales and specifically accounts for small-scale spatial and temporal patterns of GW-SW exchange. Methods to assess these patterns such as the use of natural tracers (e.g. heat) and integrated surface-subsurface numerical models have been refined and enhanced significantly in recent years and have improved our understanding of processes and dynamics. Numerical models are increasingly used to explore hypotheses and to develop new conceptual models of GW-SW interactions. New technologies like distributed temperature sensing (DTS) allow an assessment of process dynamics at unprecedented spatial and temporal resolution. These developments are reflected in the contributions to this Special Issue on GW-SW interactions. However, challenges remain in transferring process understanding across scales. ►Rapidly growing interest in groundwater-surface water exchange processes. ►Research on groundwater-surface water interactions has become multidisciplinary. ►New focus on linkages between hydrology, biogeochemistry and ecology. ►Development of new methods and models to quantify spatial and temporal patterns. ►Challenges remain in transferring process understanding across scales.