Operation of the Willamette Project impacts habitat that is important for healthy salmon. It degrades rearing, holding, and spawning habitat below the dams, reducing the abundance and productivity of listed Upper Willamette Chinook salmon and Upper Willamette steelhead. Lack of upstream and downstream fish passage at the Willamette Project dams also prevent safe access to historical breeding and rearing habitat, restricting most of the fish to habitat below the dams.

A key habitat strategy of the Willamette Biological Opinion is to work with other partners in the basin to assess needs and identify and prioritize restoration projects. In addition, the Action Agencies will plan and carry out habitat restoration programs on off-site lands to protect and restore aquatic habitat to address limiting factors for ESA-listed fish.

The Habitat Technical Team reviews potential habitat protection and restoration projects for funding using the process approved by the Independent Scientific Review Panel. In 2010, The Bonneville Power Administration provided essential funds for three of these habitat protection projects and funded one restoration project. In addition, Bonneville provided $500,000 annually for 2011-2013, increasing to $800,000 annually through 2023 for habitat restoration and protection.