Strong stratification renders the central Arctic Ocean oligotrophic, yet microbial respiration often exceeds local primary production, implying an external supply of organic carbon from productive shelves. It remains unclear whether shelf-derived dissolved organic carbon (DOC) persists in a bioavailable form during transport to the basin. Here, we combine amino acid-based molecular indicators with hydrographic analyses to trace bioavailable DOC from the Beaufort shelf into the Canada Basin. Semi-labile DOC was dominant in the upper 200 m (15–36 μmol L−1), whereas labile DOC was scarce and spatially heterogeneous (< 1.4 μmol L−1). Along halocline transport pathways from shelf to basin, semi-labile DOC declined by 25–28%, accompanied by progressive microbial alteration. Off-shelf export of semi-labile DOC could support up to 32% of the annual microbial carbon deficit in the Canada Basin. These findings highlight the halocline as an important conduit linking shelf-derived carbon to microbial metabolism in the Arctic Ocean.