It drains part of the Cascade Range east of Eugene and flows westward into the southernmost end of the Willamette Valley.

[9] The McKenzie River originates as the outflow of Clear Lake in the high Cascades of eastern Linn County in the Willamette National Forest.

Fish Lake's main tributary is Hackleman Creek, which drains the north side of Browder Ridge east of Tombstone Pass.

The McKenzie River flows south from Clear Lake, paralleled by Oregon Route 126, and goes over the Sahalie and Koosah waterfalls to Carmen Reservoir, a man-made lake from which the river is then diverted into a 2-mile (3.2 km) tunnel to Smith Reservoir.

[10][11] Between Carmen Reservoir and Tamolitch Falls, the riverbed is dry for 3 miles (4.8 km) because lava from Belknap Crater buried that stretch of the river about 1,600 years ago.

The upper basin, in the high Cascades, consists of granular, permeable igneous rocks that are geologically young, while most of the middle and lower McKenzie valley in the Western Cascades is made of the remnants of older, more weathered volcanic rocks.

[14] Principal sources of contaminants in the McKenzie are agriculture and residential development, including septic systems.

[15] Small amounts of herbicides detected in the river and some of its tributaries may be from aerial spraying by timber companies for forestry.

Along the lower McKenzie, however, winter rain slides easily off the less permeable rock and erodes sediment into the river.

The 60-mile (97 km) stretch of the river from the edge of the Springfield metro area eastward to the Cascades is known as the McKenzie Valley.

[24] The following communities, listed west to east, are in the valley: Cedar Flat, Walterville, Deerhorn, Leaburg, Vida, Nimrod, Finn Rock, Blue River, Rainbow, McKenzie Bridge, and Belknap Springs.

In more recent history, Kalapuya and Molala tribes lived nomadically in the summer and spent winters in the lower valley.

The company had established a post in 1811 at Fort Astoria at the mouth of the Columbia River for the Astor Expedition.

[19] Fish in the McKenzie River and some of its tributaries include spring Chinook salmon, mountain whitefish, and bull, cutthroat and rainbow trout.

[26] The threatened northern spotted owl inhabits dense forest on the west side of the upper McKenzie basin in Linn County.