Evolution of DOM molecular fingerprints from a river to ocean continuum: a comprehensive view of water columns, surface sediments, and chemically dark matter

Dissolved organic matter in estuarine sediments (SDOM) mediates carbon transformation and exchange across the sediment–water interface, yet its controls and fate remain poorly constrained. Here, we characterized SDOM along the Changjiang Estuary–East China Sea continuum using ultrahigh-resolution mass spectrometry, integrating prior stable and radiocarbon constraints to track SDOM provenance and age and to evaluate sediment–water exchange with co-located bottom-water DOM. SDOM was more biologically labile than bottom-water DOM, enriched in aliphatic, low-molecular-weight, nitrogen-containing compounds. We further examined chemically unassigned mass peaks (“dark matter”), which accounted for a substantial fraction of molecular richness but contributed a smaller share of bulk signal intensity. A sizable subset of these peaks was shared between sediments and the water column, indicating transferable sedimentary molecular fingerprints across the sediment–water interface. Spatial patterns identify the inner-shelf mobile mud zone as a hotspot where hydrodynamic disturbance and resuspension promote particle-mediated adsorption–desorption and rapid exchange, coupling the redistribution of fresh marine DOM with nearshore attenuation of terrestrial-derived signals. These results position SDOM as a reactive carbon pool in river-dominated margins and show that incorporating chemically dark matter yields a more complete molecular view of sediment–water DOM exchange.