Stable carbon (δ13C) and nitrogen (δ15N) isotope analysis was conducted on modern and archaeological polar bear bone collagen from the Canadian Arctic Archipelago to investigate potential changes in polar bear foraging ecology over four-millennia. Polar bear δ13C values showed a significant decline in the modern samples relative to all archaeological time-bins, indicating a disruption in the sources of production that support the food web, occurring after the Industrial Revolution. The trophic structure, indicated through δ15N, remained unaltered throughout all time periods. The lower δ13C observed in the modern samples indicates a change in the relative importance of pelagic (supported by open-water phytoplankton) over sympagic (supported by sea ice-associated algae) primary production. The consistency in polar bear δ13C through the late Holocene includes climatic shifts such as the Medieval Warm Period (MWP, A.D. 950–1250) and the early stages of the Little Ice Age (LIA, A.D. 1300–1850). These findings suggest that polar bears inhabit a food web that is more pelagic and less sympagic today than it was through the Late Holocene. We suggest that modern, anthropogenic warming has already affected food web structure in the Canadian Arctic Archipelago when modern data are contextualized with a deep time perspective.