A significant fraction of the global carbon flux to the ocean occurs in River-dominated Ocean Margins (RiOMar) although large uncertainties remain in the cycle of organic matter (OM) in these systems. In particular, the OM sources and residence time have not been well clarified. Surface (0–1cm) and sub-surface (3–4cm) sediments and water column particles (bottom and intermediate depth) from the Rhône River delta system were collected in June 2005 and in April 2007 for a multi-proxy study. Lignin phenols, black carbon (BC), proto-kerogen/BC mixture, polycyclic aromatic hydrocarbons (PAHs), carbon stable isotope (δ13COC), and radiocarbon measurements (Δ14COC) were carried out to characterize the source of sedimentary organic material and to address degradation and transport processes. The bulk OM in the prodelta sediment appears to have a predominantly modern terrigenous origin with a significant contribution of modern vascular C3 plant detritus (Δ14COC=27.9‰, δ13COC=−27.4‰). In contrast, the adjacent continental shelf, below the river plume, seems to be dominated by aged OM (Δ14COC=−400‰, δ13COC=−24.2‰), and shows no evidence of dilution and/or replacement by freshly produced marine carbon. Our data suggest an important contribution of black carbon (50% of OC) in the continental shelf sediments. Selective degradation processes occur along the main dispersal sediment system, promoting the loss of a modern terrestrial OM but also proto-kerogen-like OM. In addition, we hypothesize that during the transport across the shelf, a long term resuspension/deposition loop induces efficient long term degradation processes able to rework such refractory-like material until the OC is protected by the mineral matrix of particles.