This area is one of the most important avian migration funnels in North America. Each fall, like colorful clockwork, the refuge is the scene of a spectacular drama as millions of songbirds and monarch butterflies and thousands of raptors converge at the tip of the peninsula on their voyage south. Favorable weather patterns push migrating species through the area in waves. Clouds of tree swallows swirl over ponds and flame orange and black-winged monarch butterflies float aloft.

Protected habitats such as these provide critical stopover areas where birds and butterflies can rest and feed before resuming their arduous journey.

The strategic location at the mouth of the Chesapeake Bay encouraged military uses of the area in the years before the refuge was established. At the beginning of World War II, much of the land which is now refuge was acquired by the federal government and named Fort John Custis, after a prominent eighteenth century resident of Northampton County. During the war, large bunkers housed 16-inch guns designed to protect naval bases and shipyards in Virginia Beach and Norfolk. In 1950, the U.S. Air Force acquired Fort John Custis, renaming it the Cape Charles Air Force Station. Radar towers and additional buildings were built by the Air Force, which occupied the area until 1981.