Surface-subsurface connectivity plays an important ecological role in maintaining the structure and function of riverine ecosystems. The riverbed within wetted channels is the interface between the surface and subsurface zones, through which various types of matter and energy exchange occur. Although knowledge about the ecological importance of surface-subsurface connectivity has accumulated substantially in recent decades, progress is far behind that of surface zones, hindering a holistic understanding of river ecosystem integrity and its consideration in river management. I showcase recent progress in this field in two gravel-bed river systems in Hokkaido, Japan. First, in the Toyohira River, the chemical characteristics and sources of groundwater upwelling and the cascading effects of groundwater on the river riparian food web in a lowland section were elucidated with the aid of stable isotope ratios of carbon, nitrogen, and oxygen (together with hydrogen). The results showed that water sources are from an unknown subsurface aquifer possibly connected to a tributary, and nutrient-rich groundwater cascading effects reached riparian arthropods. Furthermore, there are indications that this connectivity affects other ecosystem properties, such as Salmonidae fish habitats. Second, in the Satsunai River, insect emergence was caught in extensive trapping and quantified over several years to highlight the insect emergence fluxes from the subsurface zone relative to the surface zone, with the aid of COI gene barcoding of various insects at larval and adult life stages. The results demonstrate that subsurface-originated insect emergence accounted for >50% of the matter flux from the river to the riparian zone. Furthermore, this diverse emergence was maintained by the presence of diverse emergence pathways associated with gravel-bar landforms. These findings collectively underscore the underrepresented ecological functions of diverse surface-subsurface connectivity in rivers and their conservation and proper management.