Dissolved organic matter (DOM) in marine sediment pore waters derives largely from decomposition of particulate organic matter and its composition is influenced by various biogeochemical and oceanographic processes in yet undetermined ways. Here, we determine the molecular inventory of pore water DOM in marine sediments of contrasting depositional regimes with ultrahigh-resolution mass spectrometry and complementary bulk chemical analyses in order to elucidate the factors that shape DOM composition. Our sample sets from the Mediterranean, Marmara and Black Seas covered different sediment depths, ages and a range of marine environments with different (i) organic matter sources, (ii) balances of organic matter production and preservation, and (iii) geochemical conditions in sediment and water column including anoxic, sulfidic and hypersaline conditions. Pore water DOM had a higher molecular formula richness than overlying water with up to 11,295 vs. 2114 different molecular formulas in the mass range of 299–600 Da and covered a broader range of element ratios (H/C = 0.35–2.19, O/C = 0.03–1.19 vs. H/C = 0.56–2.13, O/C = 0.15–1.14). Formula richness was independent of concentrations of DOC and TOC. Near-surface pore water DOM was more similar to water column DOM than to deep pore water DOM from the same core with respect to formula richness and the molecular composition, suggesting exchange at the sediment–water interface. The DOM composition in the deeper sediments was controlled by organic matter source, selective decomposition of specific DOM fractions and early diagenetic molecule transformations. Compounds in pelagic sediment pore waters were predominantly highly unsaturated and N-bearing formulas, whereas oxygen-rich CHO-formulas and aromatic compounds were more abundant in pore water DOM from terrigenous sediments. The increase of S-bearing molecular formulas in the water column and pore waters of the Black Sea and the Mediterranean Discovery Basin was consistent with elevated HS- concentrations reflecting the incorporation of sulfur into biomolecules during early diagenesis. Sulfurization resulted in an increased average molecular mass of DOM and higher formula richness (up to 5899 formulas per sample). In sediments from the methanogenic zone in the Black Sea, the DOM pool was distinctly more reduced than overlying sediments from the sulfate-reducing zone. Bottom and pore water DOM from the Discovery Basin contained the highest abundances of aliphatic compounds in the entire dataset; a large fraction of abundant N-bearing formulas possibly represented peptide and nucleotide formulas suggesting preservation of these molecules in the life inhibiting environment of the Discovery Basin. Our unique data set provides the basis for a comprehensive understanding of the molecular signatures in pore water DOM and the turnover of sedimentary organic matter in marine sediments.