The most direct effect that dams on the Columbia have on the terrestrial species of the the area is the damage that they cause to the riparian zones. The riparian zones are the dense grassy areas along the river that harbor a wide variety of wildlife. When a reservoir is created upstream from a dam the riparian zones in the area are flooded. Downstream the water level is lowered and the pace of the water is slackened which also damages this rich ecological niche. The animals that are effected by this change in habitat encompasses almost all of those who reside in the Columbia river basin. Elk, deer, and smaller mammals feed on the lush vegetation found there. Birds such as the ring necked pheasant, geese, great blue herons, hummingbirds, and many others feed there often on the teaming amphibian and insect populations that reside in the riparian zones. Riparian zones offer fertile and essential hunting ground for endangered bald eagles and peregrine falcons, and also bears, mountain lions, and kit foxes to name a few predators. Without these riparian zones the species that are equipped to move inland do so (species like pheasant and grouse require cover to survive and cannot move to higher and more open ground). If these species survive inland they can then alter the delicate balance in the forest or mountain ecosystems producing a ripple effect caused by large dams like the Bonneville.
Dams on the Columbia have seriously injured the once abundant salmonid populations that are native to the area. The shortage of salmon in the river takes its toll on many of the predators mentioned above particularly the raptors and bears. These predators relied heavily on the annual migrations of the salmon, without this easy food source they are put at a serious risk especially before the cold winter months.
The Bonneville and other hydroelectric dams have some serious impacts on the Columbia river estuary farther downriver. A recent study has shown high levels of polychlorinated biphenyls (PCB's) in the eggs, blood, and carcasses of bald eagles in the area as well as in many of the fish that they feed on. PCB's act in the same way as high concentrations of DDT, in that they cause the eggshells of nesting bald eagles to become so fragile that they are broken before the juvenile birds are mature enough to hatch. The most probable source for this contaminant is in the circuit breakers of large hydroelectric dams upstream like the Bonneville.