The Jefferson River is located in southwestern Montana and includes drainage from the Highland Mountains to the west, the Bull and Elkhorn Mountains to the north, and the Tobacco Root Mountains to the south and east. The Ruby, Beaverhead and Big Hole rivers converge to form the Jefferson River just north of the town of Twin Bridges. The area of interest to the Jefferson River Watershed Council includes the Jefferson River from the headwaters downstream to Cardwell, Montana. The Boulder River watershed, a major tributary to the Jefferson River is excluded.
The Jefferson River watershed from the headwaters at Twin Bridges to Cardwell encompasses approximately 469,994 acres. Landownership is 57% private, 28% Forest Service, and 15% State Lands and Bureau of Land Management combined. Rangeland and forested areas are the primary land uses, while agriculture comprises around 15% of the landuse. The majority of agricultural production in the valley is irrigated hayland.