Narwhals (Monodon monoceros) are sentinel species in the Arctic and to investigate marine food web changes from 1982–2011 we examined diet using fatty acids, δ15N, and δ13C, in narwhals from Baffin Bay (BB) and northern Hudson Bay (NHB). We predicted temporal changes would be greater in NHB due to a significant reduction in summer ice cover. In NHB, δ15N significantly increased, δ13C displayed a parabolic trend, and fatty acids gradually shifted, albeit not significantly, over time. δ15N was stable, δ13C decreased, and fatty acids significantly changed over time in BB. Stable isotope mixing models indicated a dietary reduction in capelin and increase in Greenland halibut from 1994–2000 to 2006–2011 in BB, while capelin was an important dietary component for narwhals in NHB in recent years (2006–2011). These dietary changes may be attributed to changes in sea ice and narwhal migration. Seasonal dietary changes, as evidenced by changes in blubber fatty acids and skin and muscle stable isotopes, were not as apparent in the NHB population, which may be indicative of a reduced migratory distance. Long-term monitoring of narwhal diet and migratory patterns associated with reduced sea ice provides invaluable information about how the marine ecosystem will redistribute with global warming.