Species and their abundance change with the seasons. The protected coves and submerged aquatic grasses provide excellent winter habitat for migratory waterfowl. Wintering species on the refuge include: black ducks, pintail, mergansers, long-tailed ducks, scoters, bufflehead, Canada geese, and tundra swans.

During the spring and summer, the salt marsh grasses, abundant insects, and submerged vegetation attract black ducks, mallards, gadwall, and green-winged teal to nest on the refuge. Gulls, terns, black skimmers, oystercatchers, and willets nest and feed along the marsh grasses, mud flats, and sand bars.

The wooded ridges provide nest sites for several waterbirds. Ten different species, including herons, egrets, and glossy ibis have been seen in rookeries on the refuge. Rookeries are groups or colonies of birds that nest together.

The marshes of Martin Refuge support an assortment of other species of wildlife. Small populations of red fox, muskrat, mink, otter, voles, northern diamondback terrapin, and various nonpoisonous water snakes exist. Other species such as clapper rails, sea-side sparrows, and marsh wrens also depend on the protected refuge habitat. Additionally, the marsh and estuary are important in the production of marine species such as crabs and oysters.

The acres of rich marsh grasses attracted settlers to the island, who raised cattle on the island and parts of the current refuge until the 1950's. Evidence of low dikes built to hold back the tide and corrals still can be seen. Two early settlers were John Evans and John Tyler. Evans and Tyler are still among the most common surnames of Smith Island residents.

Ospreys have nested at Martin for many years, and are by far the most abundant raptor. The establishment of nesting platforms for this "fish hawk" has helped to significantly increase their numbers over the years. Young birds are banded every summer in the hopes of gaining more information about the ecology of this bird of prey.

Two nesting towers for peregrine falcons have also been erected at Martin. Six captive-reared falcons were released from one of these towers in 1984. An adult pair found the tower on their own in 1986, and falcons have been nesting at Martin every since, fledging over 30 chicks from the two towers. These nests are monitored and the chicks are banded annually.

Research on black ducks began in 1995. This species has suffered declines since the 1950's due to human-induced habitat loss, degraded environment, and destruction of feeding areas. By radio-tracking the black ducks' movements, refuge personnel hope to gain enough knowledge of their day-to-day activities to create a management strategy that will increase black duck populations.

Martin Refuge will also be one of the first sites to test new methods of erosion prevention and marsh restoration developed by the U.S. Fish and Wildlife Service and the Army Corps of Engineers. Extensive island armoring and marsh revitalization is planned for the near future to prevent the loss of the critical habitats found at this refuge.