Adults of the marine-originated amphidromous goby (Gymnogobius petschiliensis) inhabit both freshwater and brackish-water areas, unlike many other amphidromous species, which spend their entire lives, except the larval stage, in freshwater. Furthermore, adult G. petschiliensis individuals incur higher osmoregulatory costs in freshwater than those in hypertonic brackish water under laboratory conditions, suggesting that the ecology of the species is largely dependent on high-salinity (ancestral) environments. Therefore, a detailed information on the ecology of G. petschiliensis will help elucidate the diversity and evolution of amphidromy. Here, this study assessed the habitat use and freshwater dependency of G. petschiliensis in two streams in central Japan. Year-round surveys showed that adult density was higher in freshwater than in brackish water during the non-spawning season. This implies that adults chose salinity habitats according to ecological conditions (e.g. inter- and intraspecific competition, and predation risk) without being bound by physiological preferences. Conversely, most egg clutches were found in brackish water. Furthermore, adult density in brackish water increased with the increase in spawning events, suggesting that the adults migrated downstream for spawning. This preference for spawning in brackish water rather than in freshwater may be attributed to the constraints of their reproductive physiology.