As a route of western expansion, the Missouri River had few equals. Lewis and Clark spent three weeks, from May 24 through June 13, 1805, exploring the segment that is now the Upper Missouri National Wild & Scenic River. Today this portion is considered to be the premier component of the Lewis & Clark National Historic Trail. Captain Clark wrote about the badlands saying, “This country may with propriety, I think, be termed the Deserts of America, as I do not conceive any part can ever be settled, as it is deficient in water, timber, and too steep to be tilled.” Of the White Cliffs, Captain Lewis wrote, “The hills and river clifts, which we passed today exhibit a most romantic appearance . . .” and described ” . . . eligant ranges of lofty freestone buildings, having their parapets well stocked with statuary . .” and “. . . seens of visionary enchantment (sic) . . . .” They spent days at the mouth of the Marias River trying to resolve the dilemma of which river to follow.

During the years following the passage of the Lewis and Clark Expedition, the Blackfeet Indians showed such an uncompromising hatred for Europeans that the Blackfeet effectively prevented the penetration of their territory by trappers. The American Fur Company was finally successful in opening the upper river to trade in 1831. In that year they established Fort Piegan at the mouth of the Marias River. The following year they moved eight miles up river and established Fort McKenzie. In 1844, McKenzie was abandoned and operations were moved down river to the mouth of the Judith River, and Fort Chardon was established. In 1845, Fort Chardon was abandoned and Fort Lewis was established a few miles above Fort Benton. In 1846, Fort Lewis was abandoned and they moved a few miles down river and established Fort Clay. At a Christmas party in 1850, Fort Clay was renamed Fort Benton.

The confluence of the Judith and Missouri Rivers was the setting for two important peace councils. In 1846, Catholic missionaries Father Pierre-Jean de Smet and Father Nicholas Point celebrated Mass for the Flathead and Blackfeet tribes to pacify relations between these traditional enemies. In 1855, Washington Territorial Governor Isaac Stevens conducted a treaty council with the Blackfeet, Flathead, Gros Ventre and Nez Perce. This treaty established boundaries and provided for railroads, roads, telegraph lines and military post access across what is now northern Montana.

The fur trade era stimulated the first extensive use of the Missouri River as an avenue of transportation. Keelboats, mackinaws, bullboats and canoes plied the upper river bringing trade items and returning with a wealth of furs. The vast amounts of capital to be obtained encouraged steamboat captains to brave the treacherous Missouri. Steamboats arrived on the scene in 1859, and Fort Benton was established as the head of navigation in 1860. The steamboats arrived just in time to supply the gold camps in southwest Montana and northern Idaho. Before commercial steamboat traffic disappeared from the scene in 1891, supplies unloaded in Fort Benton were being freighted as far west as Fort Walla Walla in Washington and north to the Great Slave Lake in the Northwest Territories.

The railroad reached Fort Benton in 1887. The last commercial steamboat arrived there in 1890. By then the buffalo had disappeared from the plains to be replaced by livestock. Fort Benton changed from being a river port to an agricultural supply center. Homesteaders began arriving in large numbers around 1910.

Following the breakout of war in Idaho, nearly 800 Nez Perce (men, women, children and the elderly) spent a long and arduous summer fleeing U.S. Army troops, first east toward Crow allies in Montana, and then north toward refuge in Canada. They crossed the Missouri River near Cow Island, which is now within the Monument, and continued up Cow Creek until they were within forty miles of the Canadian border. Thinking they were safe, they paused for a short time to rest after their arduous journey of over 1,000 miles. However, the Army troops caught up with them at what is now the Bear Paw Battlefield north of the Monument. Following a five-day battle and siege, the Nez Perce ceased fighting at Bear Paw on October 5th, 1877, in which Chief Joseph gave his immortal speech: “From where the sun now stands, I will fight no more forever.”