This dataset contains compound-specific isotope analyses of sediments from core ARA04C/37, collected from the Canadian Beaufort Sea (70°38.0212′N, 139°22.0749′W; 1173 m depth) during the ARA04C cruise in 2013. The data spans the last 14,000 years and focuses on reconstructing sea surface salinity during the Younger Dryas in the Canadian Beaufort Sea. The analyses include the hydrogen isotopic composition of both short-chain fatty acids (C16:0 and C18:0) and long-chain fatty acids (C28:0 and C30:0), as well as microalgal biomarkers (brassicasterol and dinosterol). Additionally, radiocarbon content of the short-chain fatty acid C16:0 is included. The hydrogen isotopic analyses were conducted at the University of Washington in 2020, while radiocarbon dating was performed at AWI in 2018 using the AWI MICADAS facility.