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Montana rivers — the Jefferson–Beaverhead–Red Rock in the southwest corner.

Jefferson River near Parrot Castle, October 2007

Confluence of Beaverhead and Big Hole Rivers forming the Jefferson near Twin Bridges, Montana

The Jefferson River is a tributary of the Missouri River, approximately 77 miles (124 km) long, in the U.S. state of Montana.

It and the Madison River form the official beginning of the Missouri at Missouri Headwaters State Park near Three Forks, Montana. It is joined 0.6 miles (1.0 km) upstream (northeast) by the Gallatin.

Lewis and Clark visited the site on 28 July 1805. Meriwether Lewis in his journal entry wrote:

Both Capt. C. and myself corresponded in opinon with rispect[sic] to the impropriety of calling either of these [three] streams the Missouri and accordingly agreed to name them after the President of the United States and the Secretaries of the Treasury and state.

The Lewis and Clark decision not to call the Jefferson (named for President Thomas Jefferson) the Missouri has spurred debate over what is the longest river in North America since the Missouri and Mississippi are nearly identical in length. The Missouri traditionally had been called the longest river in North America. However, 72 miles (116 km) of it have been trimmed off in channeling so that it is now sometimes referred as second to the Mississippi in terms of length. If the Jefferson were included in the Missouri length, it would still be considered the longest river.

The utmost headwaters of the Missouri are subject to debate but both locations ultimately drain into the Jefferson. Lewis on August 12, 1805, said he visited the headwaters on Trail Creek just above Lemhi Pass on the Continental Divide in the Beaverhead Mountains at around 8,600 feet (2,600 m) which he described:

the most distant fountain of the waters of the mighty Missouri in surch[sic] of which we have spent so many toilsome days and wristless[sic] nights.

However in 1888 Jacob V. Brower, who had championed turning the headwaters of the Mississippi River into a Minnesota state park, visited another site which today is believed to be the furthest point on the Missouri — now called Brower's Spring. Brower published his finding in 1896 in "The Missouri: Its Utmost Source."

Brower's Spring lies at around 8,800 feet (2,700 m) in the Centennial Mountains. The site is marked by a rock pile at the source of Hell Roaring Creek which flows into Red Rock River. ^[1] The Red Rock River rises in the Centennial Mountains near the Continental Divide in southwestern Beaverhead County, near Montana's border with Idaho. It flows west through Upper and Lower Red Rock lakes, then NNW past Lima to the Clark Canyon Reservoir, where it becomes the Beaverhead River. As the Beaverhead, the river flows NNE past Dillon. Near Twin Bridges, the Beaverhead is joined by the Ruby River and the Big Hole River, and continues as the Jefferson River north and east. Near Cardwell, it receives the Boulder River, and flows east to form the Missouri where it meets the Madison and Gallatin northeast of Three Forks, approximately 28 miles (45 km) WNW of Bozeman.

• Jefferson River Watershed Council — The mission of the Jefferson River Watershed Council is to coordinate efforts, through a spirit of community cooperation and sharing, that will enhance, conserve, and protect the natural resources, quality of life, and economic vitality of the Jefferson River watershed.^[2]
• Trout Unlimited — Trout Unlimited's mission is to conserve, protect and restore North America's coldwater fisheries and their watersheds.^[3]
• Western Watersheds Project — The mission of Western Watersheds Project is to protect and restore western watersheds and wildlife through education, public policy initiatives and litigation.^[4]
• Montana River Action — The clean flowing waters of Montana belong to the people and are held in trust by the State for a pollution-free healthful environment guaranteed by our Montana Constitution. Montana River Action's mission is to protect and restore rivers, streams and other water bodies.^[5]

• List of Montana rivers