Central Idaho retains some of the highest-quality fish habitat due to its remoteness and high elevation. Few anadromous fish can take advantage of these habitats, however, because fish passage is impeded by over 450 large dams, as well as many smaller ones, in the basin. Dams restrict the migration of anadromous fish species, blocking them from important habitats and increasing mortality of juvenile salmon traveling downstream. Some of these dams have fish passage facilities, but many smaller dams do not. Turbines kill juvenile fish.
Dams also cause migrating fish to spend more time in slower and warmer waters created by reservoirs.
Physiological stress and increased susceptibility to predators result as fish congregate in smaller areas. Public and private water managers are working to increase the survival of these fish by increasing water flows during certain times of the year to help fish travel over the dams, installing fish ladders to guide fish around the spillways, and hauling juvenile fish around dams in trucks or barges. Despite these efforts, however, dams still pose the greatest threat to the survival of native salmon and trout runs in the Columbia River Basin. Loss and fragmentation of diverse habitat have also contributed to a decline in native fish diversity. Many salmon species inhabit a small portion of their former ranges, while many introduced nonnative species, including recreational species such as bass and brook trout, are widespread.