We aimed to determine the effects of future desalination on survival of the early life stage of the littoral herbivore Idotea balthica. After collecting egg-bearing Idotea from three Baltic Sea populations, we exposed half of each brood to two either current (6 psu) or future salinity (3.5 psu). We genotyped a subsample of each brood (RAD-sequencing) to analyse patterns of allelic change and to identify genomic regions targeted by selection. The survival was reduced by hyposalinity suggesting poor tolerance to future climate. Broods within populations varied in survival to hyposalinity implying genetic variation in tolerance, with a stronger decrease in genetic diversity in future salinity. Finally, we identified proteins with crucial roles in cellular functions such as DNA replication, cell and growth. This study indicates that the future northern Baltic Sea hyposalinity will not just hamper I. balthica survival, but its selective pressure may also affect genetic diversity and cell physiology.