The main stem of the Payette River is shown on USGS topographic maps as beginning at the confluence of the South and Middle forks.

The main stem flows south from Banks for 15 miles (24 km) to Horseshoe Bend, then west into Black Canyon Reservoir.

The river's watershed was originally settled by the Shoshone, Nez Perce, Paiute and Bannock Native American groups.

In spring and summer, they temporarily moved to the lush area of lakes and wetlands along the North Fork now known as Long Valley, where they hunted and gathered in preparation for the coming winter.

In 1844, Payette retired to Montreal, still over twenty years before settlers began to arrive in great numbers from the eastern United States.

Many of the Native Americans were unhappy with the new settlers for taking and causing damage to their lands, especially due to mining, logging, and grazing.

Demand for wooden railroad ties for the Oregon Short Line (OSL) in the 1880s increased logging operations in the area.

A splash dam was built in 1902 by the Minnesota-based Payette Lumber and Manufacturing Company on the North Fork in order to help the transportation of logs downstream.

[6] From its mouth upstream to Black Canyon Dam, the river supports a mixed fishery for coldwater and warmwater species.

The North Fork of the Payette River has been severely altered by railroad and highway construction and provides only a marginal fishery for salmonids.

There are five major impoundments in the Payette basin: Black Canyon, Sage Hen, Paddock, Cascade, and Deadwood reservoirs.

Paddock Reservoir, on Big Willow Creek, has one of the better populations of black crappie in the state and a good fishery for largemouth bass.

The lower North Fork narrows and drops 1700 feet (518 m) in the 16 miles (26 km) above Banks, providing nearly endless Class V rapids (see International Scale of River Difficulty).

To the east of Banks, the South Fork's Canyon, west of Lowman, is a challenging Class IV run for rafting.

The highway on this lower stretch of the river is on the east bank and a scenic railroad, the Thunder Mountain Line,[10] runs above the west side.