Habitat
R. flumineus is endemic to Japan where it is found in riffles and swiftly-flowing mountain streams and small rivers. Its range extends from Shizuoka Prefecture and Toyama Prefecture in Honshu to the westward tip of the island, and the islands of Shikoku and Kyushu. It is a benthic species. Where it coexists with the slightly larger Rhinogobius nagoyae, the latter tends to occupy the riffles that are its favoured habitat, and R. flumineus finds alternative locations.

