Studying mechanisms of the establishment of a population in a novel environment allows us to examine the process of local adaptations and subsequent range expansion. In a river system, detecting genetic or phenotypic differences between a freshwater and brackish water population could contribute to our understanding of the initial process of brackish water adaptations. Here, we investigated behavioral and gene expression responses to the saltwater in a freshwater and brackish water population of the freshwater snail, Semisulcospira reiniana. Although the brackish water individuals exhibited significantly higher activity in saltwater than freshwater individuals in the first week, the activity of freshwater individuals increased in subsequent weeks, suggesting that their salinity tolerance was plastic rather than genetic. We found 476 and 1,002 differentially expressed genes across salinity conditions in the freshwater and brackish water populations, respectively. The major biological process involved in the salinity response of the freshwater population was the biosynthesis and metabolic process of nitrogen containing compounds, but that of the brackish water population was influenced by the chitin metabolic process. These results suggest that phenotypic plasticity induces the brackish water adaptation in the freshwater snail by modifying salinity response in the physiological process.