An analysis of the stable isotopes of oxygen (δ18O) and hydrogen (δD) was used to examine the linkage between sea ice concentration and the migration of western arctic bowhead whales (Balaena mysticetus; WABW). We compared δ18O and δD variability along the length of WABW baleen with isotopic values of zooplankton prey from different WABW habitat, with published δ13C and δ15N data, and with historical sea ice records. Zooplankton signatures varied widely (δ18O = −13‰–56‰; δD = −220‰ to −75‰), with regional separation between winter (Bering Sea) and summer (eastern Beaufort Sea) habitats of WABW observable in δD. The δ18O and δD of WABW varied significantly along the length of baleen (δ18O = 8–18‰; δD = −180 to −80‰), confirming seasonal migration and reflecting distinct regional dietary variation in isotopes. WABW migration appears to have varied concomitant with temporal sea ice concentration (SIC) changes; in years with high SIC, the difference in δD of WABW baleen between seasonal habitats was significantly greater than low SIC periods. This work shows that SIC is not only a determinant of habitat accessibility for WABW, but baleen may also be a record of historical SIC and Arctic climate.