Abstract: Benthic organisms depend primarily on seasonal pulses of organic matter from primary producers. In the Arctic, declines in sea ice due to warming climate could lead to changes in this food supply with as yet unknown effects on benthic trophic dynamics. Benthic consumer diets and food web structure were studied in a seasonally ice-covered region of Baffin Bay during spring 2016 at stations ranging in depth from 199 to 2,111 m. We used a novel combination of highly branched isoprenoid (HBI) lipid biomarkers and stable isotope ratios (δ13C, δ15N) to better understand the relationship between the availability of carbon sources in spring on the seafloor and their assimilation and transfer within the benthic food web. Organic carbon from sea ice (sympagic carbon [SC]) was an important food source for benthic consumers. The lipid biomarker analyses revealed a high relative contribution of SC in sediments (mean SC% ± standard deviation [SD] = 86% ± 16.0, n = 17) and in benthic consumer tissues (mean SC% ± SD = 78% ± 19.7, n = 159). We also detected an effect of sea-ice concentration on the relative contribution of SC in sediment and in benthic consumers. Cluster analysis separated the study region into three different zones according to the relative proportions of SC assimilated by benthic macrofauna. We observed variation of the benthic food web between zones, with increases in the width of the ecological niche in zones with less sea-ice concentration, indicating greater diversity of carbon sources assimilated by consumers. In zones with greater sea-ice concentration, the higher availability of SC increased the ecological role that primary consumers play in driving a stronger transfer of nutrients to higher trophic levels. Based on our results, SC is an important energy source for Arctic deep-sea benthos in Baffin Bay, such that changes in spring sea-ice phenology could alter benthic food-web structure.