Surface sediments from the Changjiang Estuary and adjacent shelf were analyzed using a variety of bulk and molecular techniques, including grain size composition, sediment surface area (SSA), elemental composition (C, N), stable carbon isotopic composition (δ 13 C), n-alkanes, lignin phenols, and glycerol dialkyl glycerol tetraether lipids to obtain a more comprehensive understanding of the sources and fate of sedimentary organic carbon (SOC) in this dynamic region. Bulk N/C ratios of 0.09 to 0.15, δ 13 C of À24.4‰ to À21.1‰, branched/isoprenoid tetraether index of 0 to 0.74, n-alkane content of 0.02 to 0.37 mg g À1 organic carbon (OC), and lignin content (Λ 8 ) of 0.10 to 1.46 mg/100 mg OC and other related molecular indices in these samples indicate a mixed source of marine, soil, and terrestrial plant-derived OC in the study area. A three-end-member mixing model using principal component analysis (PCA) factors as source markers and based on Monte Carlo (MC) simulation was constructed to estimate the relative contributions of OC from different sources. Compared with traditional mixing models, commonly based on a few variables, this newly developed PCA-MC model supported bulk and biomarker data and yielded a higher-resolution OC inputs to different subregions of this system. In particular, the results showed that the average contributions of marine, soil, and terrestrial OC in the study area were 35.3%, 47.0%, and 17.6%, and the highest contribution from each OC source was mainly observed in the shelf, inner estuary, and coastal region, respectively.