The Boyer River is named for a settler who hunted and trapped in the watershed before the time of Lewis and Clark. Explorers, including Lewis and Clark, John James Audubon, and Prince Maximilian zu Wied-Neuwied, navigated through the region near the mouth of the Boyer as they traveled up the Missouri River. This area is now part of the Boyer Chute National Wildlife Refuge (NWR). This was originally an island of sand and sediment deposited in the Missouri River by the Boyer River. Gradually, the Missouri River eroded a major channel (chute) through the sediment; this came to be known as Boyer Chute, and was the preferred channel used by explorers and traders until the Missouri eventually changed its course.