The McKenzie River corridor has been home to people for over 8000 years. The Molalla and Kalapuya people traveled along the river and on ridge-tops during their annual circuit of harvesting salmon, lamprey eel, camas root, huckleberries, medicinal plants and hunting. The McKenzie River trail was one of the main travel routes to the Obsidian Cliffs, on the west side of the Middle Sister. Obsidian from the cliffs was the major trade commodity from the local people. Documented sites used by Native Americans include a toolstone quarry, seasonal camps, trails, food gathering areas, camas earth ovens, peeled bark trees, rock shelters, and religious sites. Very little information about these people's lives and languages were recorded before small-pox and fever epidemics killed almost 90% of them by 1835.
Although European trading ships had been exploring the Oregon Coast for several centuries, it was not until 1812 that the first Europeans began exploring and trapping fur animals in the southern Willamette Valley. Among them was Donald Mackenzie who, as assistant leader of the Astorian Overlanders Expedition, hunted in the area for six weeks. The first map to show his name on the river was made in 1824 by Hudsons's Bay Company who he worked for at the time. The McKenzie River is one of the few rivers in Oregon that did not retain its Native American name on this map.
In 1843 immigrants began settling along the lower reaches of "McKenzie's Fork" after traveling across the country in covered wagons on the Oregon Trail. In 1848 Caswell Hendricks settled on the banks of the river just west of Walterville. The ferry crossing he operated was used until 1908 when a covered bridge was built. This area is now the popular Hendricks Park.
The first recorded travel along the entire length of the river by Europeans was in 1853 when several scouts from “The Lost Wagon Train” found their way down the McKenzie River from the east side of the Cascades. The earliest homestead recorded in the upper McKenzie River valley was staked by James Belknap in 1861 just west of the South Fork McKenzie. A ferry across the river also operated in this area until the first Belknap Covered Bridge was built in 1890. In 1861 gold was discovered in the Blue River drainage, initiating settlement of the surrounding areas. The following year the wagon road was extended from Walterville to the upper McKenzie River, then constructed over the Cascades near the North Sister by Felix Scott Jr. In 1868 wagon road work led by John Latta and John Templeton Craig crossed the Cascades at a lower elevation, but through the lava-fields, becoming the current location of Highway 242.
In the 1870’s two hot-springs resorts were in the upper McKenzie River area, increasing recognition of the area as a tourist destination. Stage stops for the wagon-road were developed every 6 to 10 miles apart, establishing the communities that are named along the river today.
In 1893 all lands within the McKenzie River watershed not already claimed by homesteaders became part of the National Forest or Bureau of Land Management. Ridge-top meadows on these lands supported sheep-grazing through the 1930s. Increased demand for lumber resulted in steady harvest of Douglas-Fir trees between 1950's and 1990. In the late 2000s these harvest levels decreased to 10% of the 1980s levels on federal lands, due to increased protection for wildlife. Private industrial forest lands in the watershed continue to be harvested and replanted on 60 year rotations.
Automobiles began using the McKenzie River highway in the early 1900s, and soon became popular as a scenic motoring destination and for fishing lodges.
In 1911 the Eugene Water and Electric Board began using water from the McKenzie River to generate power at the Leaburg Power Plant. In the early 1960s flood-control dams were built on the South Fork of the McKenzie River, and on Blue River, creating several large reservoirs. Also in the early 1960s, EWEB built the Carmen-Smith power project on the upper McKenzie River. The highway between Clear Lake and the Santiam Pass was paved during this time also.
Three sites in the watershed are listed on the National Register of Historic Places; the Goodpasture Bridge, and Old McKenzie Fish Hatchery, both just west of Vida; and Belknap Bridge between Blue river and McKenzie Bridge. The Goodpasture Bridge was constructed in 1938 and is an example of the many covered bridges throughout Lane County. A covered bridge has been at the Belknap Bridge site since 1890 as four different bridge structures. Old McKenzie Fish Hatchery at Leaburg Lake, constructed in 1905, and now a county park. This site consists of 17 buildings and ponds, and has regional significance because it is one of only two or three such facilities still surviving in the Pacific Northwest that still appears as it did at over 100 years ago.