In 1991, NOAA Fisheries listed Snake River sockeye as endangered under the Endangered Species Act (ESA). That listing was followed by the listing of spring/summer chinook, and fall chinook as threatened in 1992. Snake River steelhead were added to the list of threatened species in 1997. NOAA Fisheries Service also designated critical habitat throughout the Snake River basin in watersheds containing ESA-listed salmon. Critical habitat for Snake River steelhead was withdrawn and is being revised, but remains in place for Snake River spring/summer and fall chinook. 

Staff in the Idaho State Habitat Office (ISHO) Office, located in Boise, Grangeville, and Salmon, Idaho, address many of NOAA Fisheries' ESA and Magnuson-Stevens Act Essential Fish Habitat responsibilities throughout the Snake River basin in Idaho. Many of the watersheds in the basin are administered by either the U.S. Forest Service or the Bureau of Land Management. Consequently, much of NOAA Fisheries' workload addresses interagency consultation under ESA Section 7 for these land management agencies.

The Idaho State Habitat Office also advises the Army Corps of Engineers, Environmental Protection Agency, Federal Highway Administration, Natural Resource Conservation Service, U.S. Bureau of Reclamation, and other federal agencies on the effects of actions they fund, authorize, or proposed that may affect listed anadromous fishes in the Snake River basin. Increasingly, the focus of the office is turning to important habitats found on private lands. Activities on non-federal lands are addressed through model watersheds and ESA Section 6 Agreements with the state. Recovery Planning in Idaho’s Snake River Basin is also dealt with in the Idaho Habitat Office.

Recovery planning for and hatchery management of the Snake River ESUs are directed by the Salmon Recovery Division. Staff from that division are co-located in Boise with the Idaho State Habitat Office. Columbia River mainstem issues such as flows and fish passage are coordinated through the Hydropower Program Division in Portland, Oregon. Species listings and delistings are addressed through the Protected Resources Division, also located in Portland.