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. 

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.