In the Pacific Northwest (PNW), many populations of wild anadromous salmonids are in serious decline. Landscape change, water pollution, introduced predators, fishing, hydropower development, hatcheries, disadvantageous ocean conditions, and other factors have led to the extinction or decline and listing of many stocks under the Endangered Species Act. In recent years, the U.S. Environmental Protection Agency (EPA) has become increasingly involved in regulatory and policy issues related to habitat alteration. The Clean Water Act has a goal to restore and maintain the physical, chemical, and biological integrity of the Nation's waters, including the protection and propagation of fish, shellfish, and wildlife. Habitat alteration is a common cause for failures of aquatic systems to meet designated uses as required by the Clean Water Act, and addressing these failures increasingly requires ameliorating the cumulative impacts of diffuse stressors including nutrient loading, sedimentation, and altered hydrologic regime. As required by the Endangered Species Act, EPA is being asked to participate in inter-agency species protection and restoration efforts where habitat issues play a key role.