Organisms have an endogenous timekeeping system to coordinate their biological processes with environmental cycles, allowing adaptation to external rhythmic changes in their environment. Modification of biological clocks could contribute to range expansion in a novel rhythmic environment. We hypothesized that populations of freshwater species near estuaries have acquired a circatidal rhythm to synchronize with the tidal cycle. Here, we compared the locomotion activity and gene expression rhythms of the freshwater snail Semisulcospira reiniana between individuals inhabiting freshwater and brackish-water areas. Individuals inhabiting brackish-water areas exhibited a rhythmic activity pattern coordinated with the tidal cycle under both field and laboratory conditions. Individuals inhabiting upstream freshwater areas showed a nocturnal activity pattern. The proportion of circadian oscillating genes was greater in freshwater than in brackish-water individuals, while that of circatidal oscillating genes was greater in brackish-water than in freshwater individuals. Interestingly, expression of 16 genes exhibited circadian and circatidal rhythms in freshwater and brackish-water individuals, respectively. Additionally, transcriptome-wide population genetic analyses supported our assumption that these two populations are genetically almost identical. These findings suggest that the slight divergence contributed to the shift in the timekeeping system, and that endogenous rhythms could differ in their periods between freshwater and brackish-water populations. Our results provide evidence of the evolution of endogenous rhythm via range expansion to novel rhythmic environment in a single species.