Migratory freshwater fish species are particularly susceptible to population decline because they rely on multiple habitats and open passages to complete their life cycle. Understanding the migratory patterns of cyprinids is thus essential for their management and conservation. Gnathopogon caerelescens, a small cyprinid species endemic to Lake Biwa (Japan), is one of the most important targets of inland fisheries. However, their abundance has dramatically decreased. By using an extensive alizarin complexone-mark-and-recapture program for of G. caerelescens juveniles, together with the collaboration of commercial fishermen, this cyprinid fish was demonstrated as: (1) migrating from a nursery lagoon toward the main lake and moving along the near-shore from spring to autumn; (2) migrating from the near-shore shallow habitats to off-shore deep habitats from autumn to winter; and (3) migrating to a nursery lagoon from off-shore deep habitats from winter to spring. These results highlighted the importance of protecting individual spawning/nursery habitats, and maintaining connectivity between each spawning/nursery habitat and the lake system.