The hazards posed by infrequent major floods to communities along the Susquehanna River and the ecological health of Chesapeake Bay remain largely unconstrained due to the short length of streamgage records. Here we develop a history of high‐flow events on the Susquehanna River during the late Holocene from flood deposits contained in MD99‐2209, a sediment core recovered in 26 m of water from Chesapeake Bay near Annapolis, Maryland, USA. We identify coarse‐grained deposits left by Hurricane Agnes (1972) and the Great Flood of 1936, as well as during three intervals that predate instrumental flood records (~1800‐1500, 1300‐1100 and 400‐0 CE). Comparison to sedimentary proxy data (pollen and ostracode Mg/Ca ratios) from the same core site indicate that prehistoric flooding on the Susquehanna often accompanied cooler‐than‐usual winter/spring temperatures near Chesapeake Bay—typical of negative phases of the North Atlantic Oscillation and conditions thought to foster hurricane landfalls along the East Coast.

Plain Language Summary

Despite the vulnerability of many mid‐Atlantic cities to flooding, including Washington D.C., few long‐term records exist to assess the risks posed by extreme, infrequent, storm events. Here we document recent and prehistoric floods on the Susquehanna River, which has the largest watershed on the U.S. Eastern Seaboard, using sediment cores collected from Chesapeake Bay. Our analysis finds that much of the Susquehanna's observed centennial‐millennial scale flood variability may be driven by the frequency of hurricane landfalls along the U.S. East Coast.