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River‐dominated marginal seas are important carbon sinks on Earth. However, their carbon sequestration capacities are changing due to increased anthropogenic perturbations. Herein, we employ substantial datasets to study the characteristics of organic carbon (OC) from the East China Sea (ECS) in 2006 and 2018 and reveal the impacts of reservoir construction on the OC deposition in this region. We show that the distribution of sedimentary OC in the ECS is primarily controlled by riverine input and seabed erosion processes. Hydrodynamic processes influence the OC deposition due to both the scouring of fine‐grained sediments and selective degradation of OC associated with the sediment mobilization. The deposition flux of OC in the ECS decreased by 48% after reservoir construction. These findings demonstrate that reservoir construction seriously affected the OC deposition in the ECS and may be applicable to river‐dominated continental shelves worldwide.