Oxygen and carbon isotope profiles of bivalve mollusks (Serripes groenlandicus and Macoma calcarea) record distinct changes of water mass properties in the Bering Strait region associated with the seasonal discharge of estuarine freshwater from Kolyuchin Bay into the western Chukchi Sea. Cycles in the δ¹⁸O profiles are correlated with shell growth bands and interpreted as annual; maximum δ¹⁸O values corresponding to coldest water temperatures coincide with dark internal bands in the shell that mark slower growth during winter. A 0.5 ‰ offset between the baseline winter δ¹⁸O values of two specimens (HX68 and HX65), at different distances from the estuarine discharge, is attributed to a difference in seawater δ¹⁸O between the two sites and indicates that the influence of the estuarine water persists through much of the year. The isotope profiles of specimen AK55, collected north of Bering Strait in the Chukchi Sea, reflect the Bering Shelf-Anadyr Water flowing from south of Bering Strait. Comparison of the δ¹³C profiles shows that HX68, collected closer to Kolyuchin Bay, has high-amplitude negative δ¹³C excursions associated with incorporation of dissolved inorganic carbon that is isotopically depleted in ¹³C, probably from terrestrial runoff. The significant positive correlation between δ¹⁸O and δ¹³C values in these specimens suggests that the properties of the ambient water masses are reflected in the stable isotope profiles. These results show that the stable isotope profiles of mollusk shells can serve as proxy indicators of water mass properties, particularly during runoff events in Arctic coastal regions that are logistically difficult to sample directly.