A rapidly warming Arctic Ocean and associated sea-ice decline is resulting in changing sea-ice protist communities, affecting productivity of under-ice, pelagic, and benthic fauna. Quantifying such effects is hampered by a lack of biomarkers suitable for tracing specific basal resources (primary producers and microorganisms) through food webs. We investigate the potential of ẟ13C values of essential amino acids (ẟ13CEAA values) to estimate the proportional use of diverse basal resources by organisms from the under-ice (Apherusa glacialis), pelagic (Calanus hyperboreus) and benthic habitats (sponges, sea cucumber), and the cryo-pelagic fish Boreogadus saida. Two approaches were used: baseline ẟ13CEAA values, i.e. the basal resource specific ẟ13CEAA values, and ẟ13CEAA fingerprints, or mean-centred baseline ẟ13CEAA values. Substantial use of sub-ice algae Melosira arctica by all studied organisms suggests that its role within Arctic food webs is greater than previously recognised. In addition, ẟ13CEAA fingerprints from algae-associated bacteria were clearly traced to the sponges, with an individually variable kelp use by sea cucumbers. Although mean-centred ẟ13CEAA values in A. glacialis, C. hyperboreus, and B. saida tissues were aligned with microalgae resources, they were not fully represented by the filtered pelagic- and sea-ice particulate organic matter constituting the spring diatom-dominated algal community. Under-ice and pelagic microalgae use could only be differentiated with baseline ẟ13CEAA values as similar microalgae clades occur in both habitats. We suggest that ẟ13CEAA fingerprints combined with microalgae baseline ẟ13CEAA values are an insightful tool to assess the effect of ongoing changes in Arctic basal resources on their use by organisms.