The Kittlitz's murrelet is a rare and mysterious seabird that nests on Kodiak's remote and rocky slopes. The Refuge has conducted a study on nesting ecology and habitat of the bird since 2008.

Most species of seabirds are colonial and nest in the cliff faces and hills along Kodiak's rocky coast. The U.S. Fish and Wildlife Service has periodically surveyed seabird colonies on Kodiak since 1975.

The Steller's Eider is currently listed as threatened under the Endangered Species Act, and is a Refuge species of conservation concern. Aerial surveys help provide an estimate of wintering populations along Kodiak's coastline.

Although Bald Eagles are common on Kodiak, the Refuge has surveyed populations since 1950, and currently carries out an aerial survey to count nesting pairs every 5 years.

In 2011, the Refuge initiated a nearshore avian monitoring study to monitor coastal bird populations. This study follows the protocol of the National Park Service's Southwest Alaska Network (SWAN) Nearshore Marine Bird Survey.

Established in the 1980s, breeding bird surveys are an annual road-system monitoring program conducted by volunteers over 2 26-mile routes between June 4th and July 4th.