It flows northeast to its confluence with the Missouri River on the North Dakota side of the border, about 25 miles (40 km) west of Williston.

[6] The Cheyenne, who lived in the areas of present-day Billings and Yellowstone County, called it Mo'éheo'hé'e (also Yellow Rocks River).

The river emerges from the mountains near the town of Livingston, where it turns eastward and northeastward, flowing across the northern Great Plains past the city of Billings.

It flooded the fertile bottomlands of the Affiliated Tribes (Mandan, Arikara, Hidatsa), damaging their economy and reducing their ability to be self-sufficient.

[11] (A subsequent 2011 Supreme Court case, in which Montana asserted ownership of Missouri Basin river bottoms, so as to collect decades of back rent from a hydropower company, is unrelated.

The region around the Big Horn, Powder and Tongue rivers is the traditional summer hunting grounds for numerous Native American tribes: Lakota Sioux, Crow, Cheyenne and Cree.

The conflict was settled with the Treaty of Fort Laramie in 1868, by which the US granted the territory of the Black Hills and the Powder River Country to the Lakota people.

But the discovery of gold in 1874 in the Black Hills, however, attracted thousands of miners who invaded the sacred grounds and competed for resources.

Terry formed a base of operations at the mouth of Rosebud Creek on the Yellowstone, but the US miscalculated the strength of the Lakota, who had gathered by the thousands along the river.

Lieutenant Colonel George Armstrong Custer departed from Rosebud Creek with the 7th Cavalry on the expedition that ended in his complete defeat by the Lakota and Cheyenne at the Battle of the Little Bighorn.

The Lakota and allies were forced from eastern Montana and Wyoming: some bands fled to Canada, while others suffered removal to distant reservations, primarily located in present-day South Dakota and Nebraska west of the Missouri River.

In the early 1870s, the Northern Pacific Railroad attempted to extend rail service along the Yellowstone to Livingston from Bismarck, North Dakota, a route proposed to cross the last of the Lakota buffalo hunting grounds.

By the early 20th century, Northern Pacific was providing train service along the river to the north entrance of the park near Gardiner.

On Friday, July 1, 2011, it ruptured about 10 miles (16 km) west of Billings at about 10:40 p.m.[14] The resulting spill leaked an estimated 1,500 barrels of oil, equivalent to 63,000 US gallons (240,000 L; 52,000 imp gal), into the Yellowstone River for 56 minutes before it was shut down.

Montana Department of Environmental Quality was monitoring an area spanning a 90-mile (140 km) stretch of the Yellowstone, from the spill site downstream to a bridge just across the North Dakota border.

[29] Wildlife officials estimate tens of thousands of fish may have died, mostly mountain whitefish, but Yellowstone cutthroat and rainbow trout have been affected.

[30] The closure is expected to cause significant adverse economic impact to businesses which depend on summer tourist and recreational activities along the river.

The first stretch, from the northern boundary of Yellowstone National Park to Carbella, Montana, was open to non-fishing recreation only to allow the fish population to recover.

[34] On January 26, 2021, the Montana Department of Fish, Wildlife and Parks closed a 200-yard (180 m) section of the Yellowstone River approximately 6 miles (9.7 km) east of Reed Point at the request of the Montana Department of Transportation (MDT), after MDT inspectors discovered the bridge that carried Twin Bridges Road (former US-10) over the river was in danger of collapse.

Fish consumption advisories were put in place due to the detection of polycyclic aromatic hydrocarbons in mountain whitefish downstream of the collapse.

Human activities, including agriculture and mining, along with natural sources, contribute to suspended sedimentation levels in plain areas.

[41] The lack of dams along the river provides for excellent trout habitat from high inside Yellowstone Park, downstream through Gardiner, the Paradise Valley, Livingston, and to Big Timber, a stretch of nearly 200 miles (320 km).

The most productive stretch of water is through Paradise Valley in Montana, especially near Livingston which holds brown, rainbow and native Yellowstone cutthroat trout as well as mountain whitefish.

From Billings downstream to the North Dakota border, anglers seek burbot, channel catfish, paddlefish, sauger, smallmouth bass, and walleye.

[42][43] The pallid sturgeon (Scaphirhynchus albus), an endangered species endemic to the waters of the Missouri and lower Mississippi River basins, is also found in the Yellowstone.