Surface water characteristics of the Beaufort Sea have global climate implications during the last deglaciation and the Holocene, as (1) sea ice is a critical component of the climate system and (2) Laurentide Ice Sheet meltwater discharges via the Mackenzie River to the Arctic Ocean and further, to its outflow near the deep-water source area of the Atlantic Meridional Overturning Circulation. Here we present high-resolution biomarker records from the southern Beaufort Sea. Multi-proxy biomarker reconstruction suggests that the southern Beaufort Sea was nearly ice-free during the deglacial to Holocene transition, and a seasonal sea-ice cover developed during the mid-late Holocene. Superimposed on the long-term change, two events of high sediment flux were documented at ca. 13 and 11 kyr BP, respectively. The first event can be attributed to the Younger Dryas flood and the second event is likely related to a second flood and/or coastal erosion.