Arctic calcifiers are believed to be particularly vulnerable to ocean acidification as the Arctic already experiences low carbonate saturations states due to low temperature and high inputs of freshwater. Here, we report the finding of dense beds of Mytilus growing in tidal lagoons and river mouths, where the availability of carbonate ions is remarkably low Ωarag < 0.5. Although these Mytilus grow in the intertidal zone, and therefore are covered by seawater during high tide, δ18O isotopes of shell carbonate were low − 2.48 ± 0.05‰, confirming that their shells were deposited under low salinity conditions, i.e., reflecting a contribution from 18O-depleted freshwater. δ18O isotopes of shell carbonate became heavier with increasing salinity, with mean values of − 0.74 ± 0.96‰ for Mytilus growing in tidal pools. We calculated, based on δ18O isotopic composition standardized to a common temperature, that freshwater accounted for 7% of the carbonate oxygen in the shells of Mytilus at the habitats with near full-strength seawater salinity compared with 25% in shells collected at sites temporarily exposed to freshwater. The composition of the periostracum revealed a trend for shells from river mouths and brackish tidal lagoons to be more depleted in polysaccharides than shells exposed to higher salinity. We conclude that the high food supply associated with riverine discharge allows Mytilus to cope with the low saturation states by using energy to calcify and modify their periostracum to protect the shells from dissolution. These findings suggest that Arctic Mytilus are highly resistant to low saturation states of carbon minerals if supplied with sufficient food.