Today, the Jefferson River retains much of its scenic beauty and wildlife diversity from the days of Lewis and Clark, yet is threatened by water use issues and encroaching development.

The geology of the Jefferson River and the surrounding mountain ranges includes some of the oldest rocks found in North America, dating back to the Archean Eon, 2.7 billion years ago.

[7] Found primarily in the Tobacco Root and Ruby ranges, these ancient rocks are metamorphic, having been highly compressed and nearly re-melted by geologic forces over eons of time.

Frequently found along the Jefferson River, these rocks include layered feldspars, gneiss, glassy quartz, heavy dark amphibolite, and sometimes marble.

Eventually, the sea receded and erosion wore away intervening geologic history until about 530 million years ago, during the Cambrian Period of the Paleozoic Era.

[7] A new sea encroached on the land, depositing sedimentary layers of limestone, dolomite, shale, and sandstone over several hundred million years.

[8] By the Mississippian Period, 340 million years ago, much of western North America was covered with a warm, shallow sea, much like the Gulf Coast of Florida today.

Small marine fossils can be found in the Madison Group limestone that makes up the steep, narrow section of the Jefferson River canyon today.

Rainwater percolated down through cracks in the limestone, dissolving rock and creating caves such as those found at Lewis and Clark Caverns State Park.

The batholith is composed of at least seven, and possibly as many as fourteen, discrete igneous rock masses called plutons, which formed beneath the Earth's surface during a period of magma intrusion about 73 to 78 million years ago during the Late Cretaceous.

[11] Upstream from the Jefferson, at Barton Gulch, a tributary of the Ruby-Jefferson River system, archaeologists excavated an extensive complex of Paleo-Indian cooking pits and earth ovens dated to 9400 RCYBP.

However, the arrival and expansion of European settlers on the east coast pushed Native Americans west, in a domino effect that extended all the way into Montana.

By 1800, the Missouri headwaters and much of southwest Montana was a crossroads frequented by the Lemhi Shoshone, Bannock, Nez Perce, Flathead, Crow, Sioux, and Piegan Blackfeet.

the land is tolerably fertile, consisting of a black or dark yellow loam, and covered with grass from 9 Inches to 2 feet high.

Possible hazards include downed trees, called "sweeps" and diversion dams constructed to channel river water into irrigation ditches.

The upper Jefferson is a much-braided, meandering river and floodplain system that supports productive farm fields, extensive cottonwood groves, rich meadows, and abundant wildlife.

The river creates diverse habitats as it naturally shifts back and forth across the Jefferson Valley, forming oxbows and swamps of various depth and age.

The upper Jefferson extends from the confluence of the Big Hole and the Beaverhead rivers approximately 44 miles downstream to the community of Cardwell.

Lacking the ability to flood or meander, this section of the river has few trees, swamps, meadows, and significantly less wildlife than the upper Jefferson.

Dams constructed upstream on the Ruby and Beaverhead rivers store surplus water from spring runoff which is released to augment natural flows during the summer irrigation season.

The unnaturally warm water, combined with excess nutrients from irrigation runoff and grazing practices, can stimulate rapid growth of algae in mid-summer, to the detriment of anglers and floaters.

Efforts to stabilize portions of the riverbank with rock, concrete, and other rip-rap materials have inhibited the river's ability to flood, meander, and form new cottonwood groves and wildlife habitat.