Samples were collected from Baffin Bay in 2008, 2015, and 2017 aboard the CSS Hudson and Amundsen research vessels. The box core and triggers cores were collected at water depths ranging from 267 to 2373 m below sea level. This dataset includes bulk geochemical and lipid biomarker proxy data from these samples. Bulk geochemical datasets include % carbon, % nitrogen and their stable isotopes as measured by EA-IRMS (Elemental Analyzer linked to an Isotope Ratio Mass Spectrometer). Lipid biomarker proxy data include highly-branched isoprenoids and sterols as measured by GC-MS (Gas Chromatograph linked to a Mass Spectrometer) and isoprenoid/hydroxylated glycerol dialkyl glycerol tetraethers as measured by HPLC-MS (High Performance Liquid Chromatography linked to a Mass Spectrometer). Highly-branched isoprenoid and sterol data are presented as concentrations whereas isoprenoid/hydroxylated glycerol dialkyl glycerol tetraethers data are presented as relative abundance. All analytical measurements were performed at the University of Colorado Boulder. Further information on the data and interpretations can be found in Harning et al. (2023).