NOAA Fisheries Service is responsible for ensuring that hydroelectric facilities don't compromise the survival of salmon and steelhead that must pass through them on their migrations to and from the ocean. The majority of hydroelectric dams lack adequate fish passage. Many dams significantly decrease the level of streamflows and destroy important fish habitat. This causes serious harm to salmon and has a long-term effect on the larger landscape. Hydroelectric dams frequently provide the largest single impact on Endangered Species Act-listed fish within a specific river basin. On the other hand, about 60 percent of the region’s electricity comes from hydropower, and other economic benefits also result from these projects.

The Federal Columbia River Power System (FCRPS) is a system of dams and reservoirs on the Columbia and Snake Rivers that provide hydroelectric power, flood control and commercial navigation as far inland as Idaho. NOAA Fisheries Service has listed most of the anadromous fish runs in the Columbia Basin for protection under the Endangered Species Act. That act requires that the FCRPS operating agencies – U.S. Army Corps of Engineers, U.S. Bureau of Reclamation and Bonneville Power Administration – insure that their actions are not likely to jeopardize the continued existence of listed salmon or adversely modify critical habitat, and that they seek NOAA Fisheries Service's biological opinion in the course of doing so. Since the first salmon runs were added to the ESA list in 1991, ESA compliance with the FCRPS has been controversial and almost continuously in litigation.