[4] The river flows west, turning southwest where it receives Talbot Creek from the right, through the high mountain valley of French Meadows.

[6][8][9] It turns south-southwest, flowing through an extremely steep canyon, descending about 1,600-foot (490 m) in 10 miles (16 km) to its confluence with Duncan Creek at 3,379 ft (1,030 m) above sea level.

[8][9] At the confluence with Duncan Creek the Middle Fork begins to turn west, winding through its rugged canyon, and flows through the small Interbay Reservoir[8] where more water is diverted for power generation.

[9] The Middle Fork continues west towards the western end of Ralston Ridge, north of Balderson Station, where it is joined by its largest tributary, the Rubicon River.

[9] The Rubicon is significantly longer than the Middle Fork above their confluence, and its drainage basin is also larger, extending to the Desolation Wilderness and draining a large part of northern El Dorado County.

[9][13] Near Foresthill the Middle Fork leaves the western boundary of the Tahoe/Eldorado National Forests and enters the Auburn State Recreation Area in the foothills of the Sierra Nevada.

[2] The Rubicon River is the largest tributary watershed, at 315.4 sq mi (817 km2), which is nearly three times the size of the Middle Fork's own drainage area above their confluence.

[2] Almost the entire watershed is forested, with the exception of the alpine zone at the highest elevations near the Sierra Crest, and some areas of grassland, range and shrub in the foothills.

There is also a number of smaller unincorporated communities including Todd Valley, Michigan Bluff, and Volcanoville, all of which began life as mining camps during the Gold Rush.

In the lower part of the watershed, below the confluence with the Rubicon River, about half of the land is privately owned, with rural residential and some logging as the major uses.

[26] Plant communities in the Middle Fork have also been impacted by grazing, mining, road construction, selection cutting of larger trees, and other human activities.

The Washoe people lived east of the Sierra Crest but sometimes ventured into the high elevations of the Middle Fork and its tributaries to hunt in summer.

Plant resources were gathered at lower elevations, with the primary staple being black oak acorns, but many native varieties of grasses, roots, herbs, seeds and berries were also used.

The Middle Fork and Rubicon River canyons provided the main route of travel during the summer hunting season in the high Sierra.

[33] Although the Spanish began exploring California in the 1700s, it was probably not until Jedediah Smith's expedition in 1827 that Europeans entered the vicinity of the upper American River watershed.

[35] In 1850, miners blasted a tunnel through a ridge, diverting the Middle Fork away from the long oxbow of Horseshoe Bar and allowing the river bed to be mined for gold.

[36] Over time, the river downcut its own bed, exposing a bedrock ledge that blocked the flow of water through the tunnel and reestablished its course through the oxbow.

[40] Prospectors exploring the side canyons of the Middle Fork soon discovered that the auriferous (gold-bearing) gravels originated from strata about 2,000 ft (610 m) above the river.

The California Water Company operated numerous hydraulic mines along the Georgetown Divide and by 1874 owned 300 miles (480 km) of ditches, flumes and pipes.

Mining had a significant environmental impact on the Middle Fork and beyond, as entire hillsides loosened by hydraulic operations sloughed down into the river and were carried into the Sacramento Valley during winter floods.

The damage to navigation and flood control was such that the state legislature banned hydraulic mining in 1884,[citation needed] but even then the sediment continued to flow.

[44] In 1906 John C. Hawver, an Auburn dentist, discovered large limestone caverns along the lower Middle Fork canyon north of Cool at a height of some 700 feet (210 m) above the river.

Some 400 specimens were removed from the site, including fossils of saber-toothed tigers, mastodons, and giant ground sloths, as well as Ice Age-era human remains.

[45][46] In 1863 William Brewer had crossed the Sierra Nevada via the Middle Fork and Squaw Valley, accomplishing what Jedediah Smith had failed to do almost 40 years earlier.

The 100-mile (160 km) long trail gained renewed attention in 1955 when Wendell T. Robie and several companions rode its entire length from Squaw Valley to Auburn in one day.

However, since there were no permanent residences in the canyon, there was no loss of human life, and the floodwaters were contained by Folsom Lake, sparing the city of Sacramento from damage.

It would have inundated numerous features along the Middle Fork including parts of the Western States Trail, American Canyon, the Mammoth Bar OHV area, and Ruck-a-Chucky Falls.

During preliminary work on the dam, a unique curved cable-stayed bridge was proposed to span the Middle Fork arm of the reservoir at Ruck-a-Chucky.

[9][57] Oxbow Reservoir (Ralston Afterbay) serves as a regulating pool to allow the hydroelectric plants to operate on a peaking schedule while releasing a relatively stable flow downstream.

The Middle Fork has whitewater rafting below Oxbow Reservoir; due to Federal hydroelectric licensing and the need to deliver water downstream for irrigation and consumption, boatable flows are released year-round, even in the most severe drought conditions.