The South Fork McKenzie River has been significantly altered in the last century. Since the 1940s, logging occurred throughout the watershed, including riparian areas, and “stream cleaning” for timber and navigation purposes was a common practice. Cougar Dam was completed in 1963 at river mile 4.2 by the US Army Corps of Engineers for flood control and power generation. Associated with construction of the dam was the straightening and channelization of the lower river with levees and riprap and filling of the floodplain with substantial amounts of fill material to raise elevation and dewater the floodplain. These impacts have led to impaired ecological conditions.

A comprehensive stream inventory survey conducted by the USFS in 2005 revealed only 17% average pool area, about a 75% loss since 1937. Similarly, wood density in the area is extremely low, less than 20 pieces per mile. The dominant substrate in both pools and riffles is cobble, which is often too large for spawning. The main-stem channel of the South Fork is relatively straight, and disconnected from side-channels. This 

results in a loss of fine sediment deposits, limiting nesting habitat for turtles and further impacting riparian functions. Although once a high functioning ecosystem, the South Form of the McKenzie river now lacks suitable habitat for Spring Chinook Salmon, Bulltrout, Pacific Lamprey, Western Pond Turtle, and other native species.

Cougar Dam:

Cougar Dam has significantly altered the biological productivity and integrity of local fish populations by obstructing migration. Original construction of the dam included both adult and juvenile fish passage facilities, however due to downstream river changes, specifically regarding temperature, adult fish no longer migrated to its base so the USACE abandoned the original fish passage facilities. In an effort to fix downstream temperature issues, a temperature control facility was built in 2005. This facility draws water from varying depths within the reservoir, mixing it to a temperature that more closely replicates pre-reservoir downstream temperatures.

With adult Spring Chinook and Bull Trout now migrating to the base of the dam in search of spawning grounds, an adult fish facility was built in 2010, which collects and transports migrating adults above the reservoir to access many miles of habitat. The new tower however, poses serious challenges for juvenile spring Chinook 

The Cougar Dam temperature control tower allows for selective withdrawal of water from different reservoir depths to more closely mimic pre-dam downriver water temperatures.

Salmon trying to migrate out to sea. All water passing Cougar Dam must flow through the tower, but flow conditions at the corner of the reservoir where the tower is located make it hard for fish to find and enter it. Passage efficiency and survival rates of those that do manage to enter the tower are not high enough to support a self-sustaining population above the dam. In 2014, the USACE installed a small-scale portable floating fish collector to help inform the decision-making and design of a future permanent downstream passage solution. The fish collector attracts and holds juvenile spring Chinook salmon until they can be transported around the dam. Plans to install a permanent fish collector are currently underway, and until both upstream and downstream passage are successful spring Chinook salmon production above Cougar Dam is very limited and they are primarily of hatchery origin.