The estuarine-inner shelf region of the East China Sea (ECS) is a major sink of the Yangtze River-derived fine-grained sediments and associated organic materials. In this work, surface sediment samples from a matrix of seventy-three sites that extend from the Yangtze River estuary (YRE) to the southern inner shelf were measured for their elemental, stable isotopic and molecular indices to provide a process-oriented study on the sources, distribution and fate of sedimentary organic matter (SOM) in this region. The results indicated that the re-suspension and alongshore transport of sediments could play a key role on the accumulation of SOM in the area. In addition to the physical reworking, the low C/N ratios and the enriched δ13C values could also be likely related to the presence of microorganism-derived organic matter (OM) and soil-derived OM. The composition and principal component analyses of the n-alkanes indicated that the majority of the riverine terrigenous SOM was primarily restricted within the mud deposits along the coastal ECS. The wide occurrence and southward increasing trend of high molecular weight n-alkanes along the coastal ECS suggest an effective preferential dispersal of the terrigenous organic components. However, the local supply of the marine-derived OM potentially promotes the subsequent degradation of these terrigenous OM, which are likely responsible for the decreasing trend of the carbon preference index (CPI25–33) from the northern YRE to the southern inner shelf. This indicates that the transported SOM from the YRE could become more homogenized as it moved toward the southern inner shelf. The presence of unresolved complex mixtures (UCM), lower Pr/Ph ratios and patterns of more stable geochemical biomarkers (hopanes and steranes) in the nearshore region reveals a petroleum contamination in the coastal environment.