A great variety of birds can be found at San Juan Island National Historical Park. Some species reside in the park year round, others are seasonal residents, and still others pass through on seasonal migrations to and from far off places. Northern harriers, red-tailed hawks, bald eagles, great horned owls, and many other birds of prey are commonly viewed in the park. Songbirds, seabirds, shorebirds and waterfowl add to the seasonal diversity. Habitats include open saltwater (American Camp); rocky shoreline (American Camp); sand and gravel shoreline (South Beach); mudflats (English Camp) and brackish lagoons (Old Town, Jakle’s, and Third lagoon); prairie (American Camp); grassy bald and rocky slope (Mt. Young); open woodland and oak savanna (Mt. Young); dry coniferous forest (American and English Camps); wet coniferous forest (north slope of Mt. Finlayson); and shrubby thicket (American Camp). A final avian habitat is aerial, the vast open airspace used by virtually all birds, especially during migration, but truly the domain of raptors, swifts and other high fliers. Mt Finlayson offers a significant aspect of the aerial habitat where oceanic breezes are deflected upward. The year-round bald eagle population is the densest in the lower 48 contiguous states. A prominent nest along the entrance drive to the American Camp visitor center fledged three eaglets in 2003, a rare feat for the species. This incredibly accessible wildlife viewing opportunity has been a highlight for visitors and islanders since 1995.

Humans have introduced numerous species of birds to the islands with varying degrees of impact on the ecosystem. California quail and wild turkey are non-natives which have established populations on the islands. Another non-native, the Eurasian Skylark, did not fare so well. Seen and heard on the American Camp prairie from 1960 until 2000, this ground nesting bird was susceptible to predation from airborne and terrestrial predators.

Human impacts such as habitat destruction or degradation; pollutants and chemicals in the air, water and land; commercial and recreational fishing; predation and harassment by dogs and cats; development; and many recreational activities take a direct or indirect toll on bird populations and individual birds.