The movement of water, matter, organisms, and energy can be altered substantially at ecohydrological interfaces, the dynamic transition zones that often develop within ecotones or boundaries between adjacent ecosystems. Interdisciplinary research over the last two decades has indicated that ecohydrological interfaces are often “hotspots” of ecological, biogeochemical, and hydrological processes and may provide refuge for biota during extreme events. Ecohydrological interfaces can have significant impact on global hydrological and biogeochemical cycles, biodiversity, pollutant removal, and ecosystem resilience to disturbance. The organisational principles (i.e., the drivers and controls) of spatially and temporally variable processes at ecohydrological interfaces are poorly understood and require the integrated analysis of hydrological, biogeochemical, and ecological processes. Our rudimentary understanding of the interactions between different drivers and controls critically limits our ability to predict complex system responses to change. In this paper we explore similarities and contrasts in the functioning of diverse freshwater ecohydrological interfaces across spatial and temporal scales. We use this comparison to develop an integrated, interdisciplinary framework, including a roadmap for analysing ecohydrological processes and their interactions in ecosystems. We argue that, in order to fully account for their non-linear process dynamics, ecohydrological interfaces need to be conceptualised as unique, spatially and temporally dynamic entities, which represents a step change from their current representation as boundary conditions at investigated ecosystems.