Return flows in river channels vary widely in subsurface residence time, ranging from deep flows associated with alluvial fans and tributary confluences to shallow flows within gravel bars, which influence habitat quality for hyporheic communities. Return flows from deep subsurface water are considered baseflow and exhibit relatively stable discharge and temperature, whereas those from shallow subsurface flows are influenced by the permeability of gravel bars and are therefore less stable. To better understand the characteristics of these variable return flows, we compared water quality and benthic fauna at the surface–subsurface interface across three habitat types (downwelling, lateral, and upwelling) in the Tenryu River. Water quality and benthic fauna differed markedly among the three habitat types and withing upwelling habitats according to the depth of subsurface flow. In addition to burrowing stoneflies and isopods, which are known as hyporheic or groundwater species, we also found migratory shrimp that appeared to have entered upwelling habitats during upstream migration.