In an effort to determine species presence, distribution, habitat use, and migratory patterns, extensive studies have been conducted in the refuge.

Biologists have studied extensively in the biologically rich Naknek River basin which provides an important habitat for thousands of ducks, geese and swans.

The Alaska Peninsula Refuge contains a number of geologic and scenic features, with a mixture of volcanic activity juxtaposed alongside glacial valleys and coasts under erosion.

In contrast to the volcanic landscape of the refuge, the Pacific coast of the protected area is characterised by rugged cliffs, bays, fjords, and streams.

In particular the Castle Cape Fjords in the Chignik area is an extremely pronounced feature, with a strong erosion by the sea, with rocks shaded in contrasting dark and light tones.

The refuge supports a diversity of fish and wildlife and is an important nesting site for seabirds such as puffins, cormorants, kittiwakes, and guillemots, emperor geese, harlequin ducks, Steller's eider, and notably the bald eagle.

[2] Alaskan brown bears are a common sight in the coastal meadows in spring and summer when they come to feed on the spawning salmon.