Before the gold rush, only a few visitors had come to the region; one of the first was explorer David Thompson, a cartographer for the North West Company. Thompson and four fellow fur traders arrived in 1808 to trade with the Lower Kootenais. The local natives gave Thompson's party dried fish and moss bread. Thompson returned the next year and established a trading post on Lake Pend Oreille. He was followed in 1846 by Jesuit Priest Father DeSmet, a missionary to the Kootenai Tribe.
On September 20, 1974, the Kootenai Tribe, headed by chairwoman Amy Trice, declared war on the United States government. Their first act was to post soldiers on each end of the highway that runs through the town and they asked people, to pay a toll to drive through what had been the tribe's aboriginal land. The money would be used to house and care for elderly tribal members. Most tribes in the United States are forbidden to declare war on the U.S. government because of treaties, but the Kootenai Tribe never signed a treaty. The dispute resulted in the concession by the United States government and a land grant of 10.5 acres (42,000 m2) that is now the Kootenai Reservation.
Bonners Ferry is 8 miles (13 km) from the site of the Ruby Ridge confrontation and siege in 1992, which occurred just outside Naples, Idaho.
In recent years, Mormon Fundamentalists from nearby Bountiful, British Columbia have established a presence in Bonners Ferry. They have brought with them the controversial practice of plural marriage.
*Not to be confused with Fairy's Boner.