The interactions of groundwater with surface waters such as streams, lakes, wetlands, or oceans are relevant for a wide range of reasons—for example, drinking water resources may rely on hydrologic fluxes between groundwater and surface water. However, nutrients and pollutants can also be transported across the interface and experience transformation, enrichment, or retention along the flow paths and cause impacts on the interconnected receptor systems. To maintain drinking water resources and ecosystem health, a mechanistic understanding of the underlying processes controlling the spatial patterns and temporal dynamics of groundwater–surface water interactions is crucial. This Special Issue provides an overview of current research advances and innovative approaches in the broad field of groundwater–surface water interactions. The 20 research articles and 1 communication of this Special Issue cover a wide range of thematic scopes, scales, and experimental and modelling methods across different disciplines (hydrology, aquatic ecology, biogeochemistry, environmental pollution) collaborating in research on groundwater–surface water interactions. The collection of research papers in this Special Issue also allows the identification of current knowledge gaps and reveals the challenges in establishing standardized measurement, observation, and assessment approaches. With regards to its relevance for environmental and water management and protection, the impact of groundwater–surface water interactions is still not fully understood and is often underestimated, which is not only due to a lack of awareness but also a lack of knowledge and experience regarding appropriate measurement and analysis approaches. This lack of knowledge exchange from research into management practice suggests that more efforts are needed to disseminate scientific results and methods to practitioners and policy makers.