Understanding the response of marine fauna to this change is critical for understanding the effects of OA. Population level variation in OA tolerance is highly relevant and important in the determination of ecosystem resilience and persistence, but has received little focus to date. In this study, whether OA has the same biological consequences in high salinity-acclimated population vs a low-salinity acclimated population of the same species was investigated in the marine isopod Idotea balthica. The populations were found to have physiologically different responses to ocean acidification. While survival rate was similar between the two study populations at a future CO2 level of 1000 ppm and both populations showed increased oxidative stress, the metabolic rate and osmoregulatory activity differed significantly between the two populations. The results of this study demonstrate that the physiological response to OA of populations from different salinities can vary. Population level variation, and the environment provenance of individuals used in OA experiments should be taken into account for the evaluation and prediction of climate change effects.