The construction of the Bonneville Dam flooded traditional Indian fishing sites that had played an integral part in their culture. In 1945, eight years after the beginning of construction, the Secretary of War transferred land to the Secretary of the Interior under the Act of March 2, 1945 (59 Statute 22). This land was then given to the Bureau of Indian Affairs as five replacement fishing sites. The Indian tribes who have use of the sites are the Yakama, Umatilla, Warm Springs, or "any other tribe that had treaty fishing rights that were inundated or destroyed by the Bonneville Dam" (25 CFR 248). Once declared eligible, the land may be used for fishing and camping by eligible parties and their families. All Federal and State laws apply in the sites, as well as any the Area Director deem necessary to impose. For example, the Area Director, "the position responsible for administration of the Portland Area of the Bureau of Indian Affairs," may prohibit the use of alcoholic beverages, use for commercial purposes, or use for cleaning fish at the site. A more detailed description of the process of becoming eligible can be found in "Indian Allotments," 43 CFR 2530, and of the use of the sites in "Use of Columbia River Indian In-Lieu Fishing Sites," 25 CFR 248.

An ongoing debate exists between Indian tribes and the States of Oregon and Washington over fishing rights. In an effort to conserve the salmon population threatened by the Bonneville, the Mitchell Act, passed close to the time of the Bonneville Project Act, encouraged hatcheries to be built on the Columbia. However, the States placed these hatcheries on the lower half of the river, below the Indian fishing sites. In the 1968 cases of Sohappy v. Smith and U.S. v. Oregon the Indians challenged the placement of the hatcheries declaring it unfair. The decision, called the Belloni decision, ruled in favor of the Indians and in 1974 Judge Bolt interpreted a "fair share" as fifty percent of all harvestable fish (A Short Chronology of Treaty Fishing on the Columbia River). These decisions were upheld by the Supreme Court in 1979.

Since this date efforts have been made by the States of Oregon and Washington to make certain that fish do reach the Indian In-Lieu Fishing Sites, although it has proven difficult to honor both environmental and tribal requirements. For example, the Columbia River Inter-Tribal Fish Comission (CRITFC), composed of Oregon police officers, patrols 147 miles of the Columbia River starting at the Bonneville Dam. They "serve as an extension of tribal law enforcement. CRITFC's constituency consists of tribal members exercising treaty fishing rights in the Columbia River Basin. Enforcing fishing regulations plays a vital role in salmon restoration" (Columbia River Inter-Tribal Fish Commission).

In other recent news, the Bureau of Indian Affairs evicted Indians living on these sites in 1995. Permanent structures were prohibited on the in-lieu fishing sites by the federal government in 1969. Individual Indians as well as the "Chiefs and Council of the Columbia River Indians" disputed this in the case of Sohappy v. Hodel. They claimed that the eviction of Indians living on the fishing sites violated terms agreed to in 1945. Chief Frederick Ike replied in response to the evictions, "They've taken everything away from us-- fishing rights, fish, the land... all we have left are in-lieu sites, and we would like to hold onto them... Salmon is our No. 1 food. In our religion, we even have songs that state that it is very sacred" ("Regional News," April 16, 1984). The Ninth Circuit reversed this portion of the Act of 1945 and moved to amend it (25 CFR 248). The evolving nature of legislation concerning Native Americans prompted by the creation of the Bonneville Dam, has affected their cultures greatly.