Marine sediments represent an important benthic source of dissolved organic carbon (DOC), yet the molecular fate of sediment-derived DOC during transfer across the sediment–water interface remains poorly constrained. Here, we used vertically connected samples of porewater, overlying water and bottom water from the South China Sea to examine how DOC molecular composition, microbial communities and metabolic potential change across this interface. DOC in porewater was compositionally distinct from DOC in overlying water and bottom water, with greater molecular diversity, higher H/C ratio, lower nominal oxidation state of carbon values and enrichment of aliphatic and lipid-like components. These features indicate that benthic diffusive fluxes introduce a reduced and compositionally distinct DOC pool into bottom waters. To resolve the fate of DOC molecules during transfer across the interface, we tracked molecular occurrence across porewater, overlying water and bottom water and classified molecules into removed, generated and persistent categories. Removed and persistent molecules dominated the porewater DOC fate distribution, accounting for 36.8% and 53.8%, respectively. Removed DOC was consistently enriched in reduced and weakly aromatic molecules, whereas persistent DOC was dominated by lignin-like components and remained detectable from porewater to bottom water. Generated DOC represented a minor but habitat-specific fraction, with cold seep samples enriched in sulfur-containing formulas. Fate-weighted flux estimates further showed that cold seeps increased the magnitude of both removed and persistent DOC fluxes, without fundamentally changing the dominant fate structure. Microbial correlations and genomic annotations linked removed DOC to substrate-specific microbial processing, including fatty acid metabolism, carbohydrate degradation and aromatic transformation. Together, these results show that the sediment–water interface is not merely a conduit for benthic DOC release, but a reactive molecular filter that selectively removes and generates DOC while permitting a persistent fraction to cross the interface. By regulating the molecular composition of DOC transferred from sediments to bottom waters, this filtering process may influence the persistence and biogeochemical role of benthic DOC in the ocean.