Organisms have an endogenous time-keeping system to coordinate their biological processes with environmental cycles and thereby adapt to external rhythmic environments. Some organisms in the tidal environment have the circatidal rhythm to cope with the tidal cycle. In the freshwater snail, Semisulcospira reiniana, we revealed that individuals inhabiting freshwater areas have the circadian rhythm in their locomotion activity and gene expression, while those inhabiting brackish water areas have the circatidal rhythm. Here, we investigated whether their endogenous rhythms are determined genetically or plastically by environmental cycles. First, we exposed snails to a simulated tidal environment with a 12-h period for a month and then measured their activity rhythms under the constant condition. Individuals in both freshwater and brackish water populations exhibited the circatidal rhythm, suggesting that tidal stimulations can induce the circatidal rhythm even in freshwater populations. Additionally, we investigated genetic differentiation between the two populations. Transcriptome-wide population genetic analyses suggested there is quite low differentiation between the two populations. Our findings suggest that the populations in freshwater and brackish water areas were genetically almost identical and the shift in the endogenous rhythm driven by phenotypic plasticity contributes to the expansion of the habitat of the freshwater snail.