A sediment core taken proximal to a large sunken ship in the north channel of the Yangtze delta suggests a dramatic change in sedimentation that is coincident with the sinking of the ship. We conducted AMS 14C and OSL dating and analysed the lithology, grain size, magnetic susceptibility and organic elemental geochemistry and combined these data with historical marine charts and historical data. A notable change in sedimentary environments implies a dramatic change to the geomorphological evolution of the environment at the location of the shipwreck. The sediments below the shipwreck layers suggest that the shipwreck occurred in a sheltered tidal channel developed at the north margin of the Tongsha Shoal of the Yangtze River mouth. The shipwreck layer containing the wood pieces of the sunken ship is composed of structureless silts and underlain by homogeneous mud separated by an erosional contact. The ship/storm layer is overlain by sandy facies reflecting a change to more open marine channel conditions. The sedimentary data implies that a large historical typhoon possibly on July 31, 1879 sunk several ships and caused significant geomorphological change to the Yangtze delta.