The study of glacial relict species has been focused on understanding how the biogeographic patterns of species have developed. A number of studies using phylogenetic and population genetics approaches have been conducted for terrestrial glacial relict species, and the mechanisms of their formation have been elucidated. On the other hand, less focus has been placed on glacial relict species inhabiting freshwater systems. In particular, stable lakes can serve as refugia during a glacial period, but research studies on freshwater relict species inhabiting lakes have not been well conducted. In order to clarify the mechanism of the glacial relict species in freshwater, we conducted a molecular phylogeny analysis, divergence time estimation, and a biogeographic reconstruction on freshwater Valvatidae molluscs, which have been considered as a glacial relict in the Japanese Archipelago. Our study shows that the valvatid fauna in the Japanese Archipelago was produced by multiple dispersal events from the Asian continent and by vicariance events during the period of the Pliocene–Quaternary glaciation. It includes multiple relict species that survived interglacial periods in different lakes. These findings suggest that the lakes can serve as refugia not only during glacial periods, but also during interglacial periods.