Hatchery operations have been generally limited to increasing total salmon numbers in the system as a whole, without regard for sustaining the historical geographic distribution of the species present. Further, hatchery operations have not effectively considered the biology of the organisms reared. Thus, salmon reared in hatcheries may learn behavior which may hinder them after release. Juveniles are often released at a single point and all at one time. Some of these juveniles may not be ready to migrate. Further, they may be released without proper acclimation and imprinting, and into streams with environments to which they are not particularly well suited.
Federal statutes such as the Federal Power Act and the Fish and Wildlife Coordination Act of 1934 and its amendments were designed to provide mitigation for damages caused by water and other federal projects. The prevailing notion behind mitigation was to move fish production from natural areas to federally and power company-funded hatcheries as hydropower development, irrigation, forestry, and mining swept across the Columbia River Basin. However, mitigation provided did not necessarily take place where the damage occurred, or for the same species that had been damaged. As a result, an imbalance was created by the geographical redistribution of individual stocks in the Columbia River Basin to areas downstream from Bonneville Dam. Subbasins that might be appropriate for reintroduction (where salmon populations have been extirpated) or supplementation (where populations are at high risk of extirpation) programs are summarized in Table 3.7.