The timing of their entry into freshwater was found using otolith Sr:Ca ratios of 172 silver eels from the Hamana Lake system of central Japan, to be an important factor affecting whether or not Japanese eels (Anguilla japonica) later leave freshwater during their early growth phase. A high degree of phenotypic plasticity in migration and habitat use during their growth phase was found, with eels living in, or moving between, both freshwater and estuarine water. Of the 59% of the total eels that entered freshwater, 23% of those moved back to the brackish water lake within about 2 years. A higher proportion of river residents were females, but there were no significant differences in size, age, or growth at the start of their spawning migration among the different migratory types. None of the earliest eels to move into freshwater appeared to move back into the lake, and none of the eels that experienced the highest salinities at the time of recruitment appeared to enter freshwater. However, a large proportion of eels that arrived in freshwater later returned to the lake. This suggested that timing of arrival into freshwater may be an important factor determining which eels entering freshwater will remain there and which will make habitat shifts back to estuarine habitat.