Landings of pond smelt in Lake Shinji showed a drastic decline in 1994 and are still at reduced levels. To provide advice on an appropriate strategy to manage this fishery, it is necessary to understand details concerning both the fish's migration patterns and its habitats throughout its life history. This study investigated migration patterns by field surveys using both set and trawl nets, and by analysing the Sr:Ca ratio of the otoliths of the fish caught. The results suggest that many individuals hatch in the inflowing rivers and during May-July migrate seaward into Lake Nakaumi or the adjacent sea. Thereafter, in January and February, they return upstream to Lake Shinji for spawning. Before seaward migration, the main habitat was in the inflowing rivers. This is in stark contrast to previous data (while pond smelt were abundant), when many of these fish were resident throughout life in Lake Shinji: a life style considered to be rare in recent years since the stock declined.