There is a trend for fish in the genus Rhinogobius to move from marine to freshwater habitats as they evolve, and R. brunneus is amphidromous (migratory) while R. flumineus inhabits land-locked river basins.

[3] R. flumineus is endemic to Japan where it is found in riffles and swiftly-flowing mountain streams and small rivers.

[1] 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.

[4] R. flumineus holds itself in a stationary position on a rock in fast-flowing water by means of a "sucker" formed from its two ventral fins.

The eggs are deposited in a nest and guarded by the male, and the newly-hatched juvenile fish live on the riverbed.