The sea was named after Robert Todd Lincoln, then United States Secretary of War, on Adolphus W. Greely's 1881–1884 Arctic expedition into Lady Franklin Bay.

Before the 1980s, only low-flying aircraft samplings and ground observations from ice islands could be attempted; these did not stray far from the shores of Greenland and the Canadian Arctic Archipelago due to the harsh environment.

Between 1989 and 1994, the field experiments in Project Spinnaker were underway, implementing instrumentation that captured temperature and salinity profiles well into the heart of the Lincoln Sea.

Taken just east of where the North American continent intersects the Lomonosov Ridge, these observations revealed the oceanographic features and current formations within and surrounding the Lincoln Sea.

From the Bering Strait, Pacific Ocean waters flow counterclockwise (cyclonically) along the northern shores of Canada, passing through the Lincoln Sea.

Measurements reveal that this undercurrent shares comparable features to that found in the Beaufort Sea, whose boundary currents are responsible for large-scale advection within the Arctic circulation.

Because of this mutual oceanographic behavior, it has been determined that the Lincoln Sea undercurrent continuously flows and is a component of the boundary current system that spans between Alaska and Greenland along the northern shores of the Canadian archipelago.

Although this represents only one of the many pathways from the Arctic Ocean basin through the Canadian archipelago, "…this [total drainage] is an order of magnitude less than the flux of sea ice out of [the] Fram Strait.

[7] In 2022, Canada and Denmark formalized the maritime boundary between Nunavut and Greenland, including in the Lincoln Sea, and establishing a land border on Hans Island.