Fort Clatsop National Memorial's strategic geographic location is responsible for the park's high biodiversity relative to its size. The park is home to more than 135 species of vertebrates, including at least 43 mammals, more than 74 birds, 10 amphibians, 9 fish, 2 reptiles, and thousands of invertebrates.
The park's most charismatic large mammals, Roosevelt elk (Cervus elaphus roosevelti), figure prominently in the site's history from the time of the Lewis and Clark expedition. The abundance of elk was a critical factor in the party's decision to winter in the area. In February of 1806 Meriwether Lewis wrote, "The Elk is the same with that found in much the greatest portion of North America, they are common to every part of this country, as well the timbered lands as the plains." Today a resident herd frequents the park's forests and willow swamps during winter, and elk are often seen loafing in nearby fields in spring and summer. Six of the Memorial's bat species and the white-footed vole (Arborimus albipes) are federal species of concern. These nocturnal mammals reside in the park's mature coniferous forests, together with northern flying squirrels (Glaucomys sabrinus sabrinus) and western red-backed voles (Clethrionomys californicus).
The park has a high number of resident and migratory birds due to its diversity of habitats and its location within the Pacific flyway. Bald eagles (Haliaeetus leucocephalus) nest near the park and can often be seen in flight or perching along the Lewis and Clark River. As a result of protection and the banning of DDT, these formerly endangered birds are making a strong comeback along the northern Oregon coast. Osprey (Pandion haliaetus), hawks, herons, migrating shorebirds, and wintering waterfowl also frequent the park's wetlands. Band-tailed pigeons (Columba fasciata) and olive-sided flycatchers (Contopus borealis), two federal species of concern, seasonally inhabit the park's coniferous forests along with resident pileated woodpeckers (Dryocopus pileatus), an Oregon sensitive species.
The park's extensive and diverse wetlands support a relatively high number of amphibians. Of 10 confirmed species, three are uncommon or rare. Imperiled due to habitat loss, the Columbia torrent salamander (Rhyacotriton kezeri) is an aquatic inhabitant of small cold streams. The Pacific giant salamander (Dicamptodon tenebrosus) lives in the park's small streams and adjacent moist forests. The northern red-legged frog (Rana aurora aurora), a federal species of concern, inhabits the park's forests and freshwater wetlands.
Several lower Columbia River salmonid fish stocks are federally listed. Of these, coho and chum salmon (Oncorhynchus kisutch and O. keta) and cutthroat trout (Oncorhynchus clarkii clarkii)have been found in park streams and sloughs. Fall Chinook (O. tshawytscha) were documented in spawning records for the Lewis and Clark River previous to 1996, but have not been encountered in more recent surveys. Future estuarine restoration projects will reestablish spawning and rearing habitat for these species.
The park's two reptiles, the northwestern and common garter snakes (Thamnophis ordinoides and T. sirtalis), may be found in all upland habitats. Several nonnative vertebrate pests occur in the park, including black rats, opossum, nutria, starlings, and bullfrogs.
Approaching, feeding, hunting or removing wildlife from the park is illegal. A current state fishing license is required to catch fish in the Lewis and Clark River, and Oregon Department of Fish and Wildlife established fishing seasons must be observed.
