Although relationships among environmental condition and life history traits have been widely studied in ectotherms, little is known about geographic variation in habitat use within a species. The ayu (Plecoglossus altivelis) is an amphidromous fish migrating between sea and rivers. We hypothesized that the ayu from lower latitudinal area mainly use brackish water as a nursery habitat in the marine stage, as high salinity combined with high temperature causes adverse effect on larval survival. In this study, 272 adults were collected from 8 rivers along the Japanese Archipelago, and the otoliths were analyzed to reconstruct growth trajectory, salinity profile, and date at upstream migration. As a result, larvae (1–80 age) experiencing low salinity had higher growth rate than those with high salinity in all populations. This trend was consistent with the result that low-latitude dwellers showed strong dependency on low salinity area. Furthermore, they showed relatively high-salinity profile after the upstream migration, indicating their occasional visit to brackish waters in the fluvial stage. This could be a behavioral response against environmental condition such as food availability, since prey biomass in both sea and rivers at lower latitude is limited comparing with higher latitude.