Alameda Point's landscape diversity and central location in the San Francisco Bay estuary make it an inviting area for wildlife, especially birds. Many of the birds that visit Alameda Point are migrating, such as the Western Sandpiper and Black-bellied Plover, and can only be spotted in the winter before they return to summer breeding areas like northern Alaska. Other birds, such as the California Brown Pelican, can only be seen in abundance during the warm months. The endangered California Least Tern can only be seen from April to mid-August while breeding on the Nature Reserve. A pair of ospreys can be seen nesting during the spring at the entrance to the Seaplane Lagoon.

A small colony of Great Blue Herons has found Alameda Point to their liking year-round, and often set up nests in cypress trees on the Nature Reserve. The undisturbed wetlands on the Nature Reserve provide habitat for shorebirds, while the mature evergreen and deciduous trees throughout Alameda Point are good places to spot everything from songbirds to raptors to butterflies. One of Alameda Point's most unique wildlife habitats is Breakwater Island - an offshore rock wall on the south side - which is the largest night roosting site for brown pelicans on San Francisco Bay. Harbor seals can be seen resting on a specially-built float near the Bay Trail on the south shore not far from the ferry maintenance facility.