Sediment cores were collected from the East China Sea inner shelf in 2010 to study the decay and preservation of organic carbon (OC). The highest sediment mass accumulation rate (0.61 ± 0.20 g cm−2 yr−1), derived from 210Pb, was found near the river mouth and decreased alongshore to the south (0.17 ± 0.004 g cm−2 yr−1), and in an offshore direction (0.31 ± 0.08 g cm−2 yr−1). Average total OC content was higher at inner shelf stations (0.52%) than those offshore (0.38%). The δ13C was more depleted at nearshore (−23.49‰ to −21.97‰) than offshore (−22.49‰ to −21.60‰) stations. Principal component analysis indicated that terrestrial OC, as indicated by lignin-phenols (Λ8) values, was preserved in sediment closer to the coast (0.22–0.44), while offshore sediment was more composed of lignin-poor (0.12–0.24) degraded OC that was likely hydrodynamically sorted. Marine-derived OC, as indicated by plant pigments, was significantly more abundant in the sediment mixed layer than the underlying accumulation layer. Historical flooding events were detected in Λ8 profiles in two of the six cores located at midshelf stations. Despite the magnitude of the 2010 flood in East China, we did not see any signature of this event with the chemical biomarker in these two cores. This may suggest that reduced sediment loading due to recent dam construction may have greatly decoupled river inputs with sediment loading to shelf sediment. The total OC standing stock since 1900 was approximately 1.62 ± 1.15 kg C m−2, about one tenth of all the middle and lower lakes in the Changjiang catchment basin. This work further supports the need for more research to better understand how the reduced inputs of fluvial input of sediments from Chinese rivers (due to river diversions and dams) affect carbon cycling in the East China Sea.