The name of the Beaverhead originates from Beaverhead Rock on the middle river. This rock formation was recognized by Sacajawea when the Lewis and Clark Expedition passed the area in 1805. There were also many beavers in the area at the time, but the name does not originate from the animal. In 1805, Captain Meriwether Lewis traveled up the Jefferson and Beaverhead first, but when the rest of the expedition came, a sign Lewis had left at the confluence of the Beaverhead and Big Hole telling them to follow the Beaverhead had been cut down by a beaver, and the expedition traveled up the Big Hole instead. As a result, the swifter current of the Big Hole swamped two of their canoes before they could travel back down to the confluence.