Marine organic matter (OM) sink sfrom surface water to the seafloor via the biological pump. Benthic communities, which use this sedimented OM as an energy and carbon source, produce dissolved OM (DOM) in the process of degradation, enriching the sediment pore water with fresh DOM compounds. In the oligotrophic deep Arctic basin, particle flux is low but highly seasonal. We hypothesized that the molecular signal of freshly deposited, primary produced OM would be detectable in surface sediment pore water which should differ in DOM composition from bottom water and deeper sediment pore water. The study focused on (i) the molecular composition of the DOM in sediment pore water of the deep Eurasian Arctic basins, (ii) the signal of marine vs. terrigenous DOM represented by different compounds preserved in the pore water and (iii) the relationship between Arctic Ocean ice cover and DOM composition. Composition based on mass spectrometric information, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were correlated with environmental parameters with partial least square analysis. The fresh marine detrital OM signal from surface water was limited to pore water from < 5 cm sediment depth. The productive ice margin stations showed a higher abundance of peptide, unsaturated aliphatic and saturated fatty acid molecular formulae, indicative of recent phytodetritus deposition, than the multiyear ice-covered stations, which had a stronger aromatic signal. The study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and how it may be altered in response to sea ice retreat and increasing river runoff.