Climate change is altering the biogeochemical and physical characteristics of the Arctic marine environment, which impacts sea ice algal and phytoplankton bloom dynamics and the vertical transport of these carbon sources to benthic communities. Little is known about whether the contribution of sea ice-derived carbon to benthic fauna and nitrogen cycling has changed over multiple decades in concert with receding sea ice. We combined compound-specific stable isotope analysis of amino acids with highly-branched isoprenoid diatom lipid biomarkers using archived (1982-2016) tissue of benthivorous Atlantic walrus to examine temporal trends of sea ice-derived carbon, nitrogen isotope baseline and trophic position of Atlantic walrus at high- and mid-latitudes in the Canadian Arctic. Associated with an 18% sea ice decline in the mid-Arctic, sea ice-derived carbon contribution to Atlantic walrus decreased by 75% suggesting a strong decoupling of sea ice-benthic habitats. In contrast, a nearly exclusive amount of sea ice-derived carbon was maintained in high-Arctic Atlantic walrus (98% in 1996 and 89% in 2006) despite a similar percentage in sea ice reduction. Nitrogen isotope baseline or the trophic position of Atlantic walrus did not change over time at either location. These findings indicate spatial differences in the restructuring of carbon energy sources utilized by Atlantic walrus and their benthic prey and in turn, a change in Arctic marine ecosystem functioning between sea ice-pelagic-benthic habitats.