Montezuma National Wildlife Refuge provides habitats for an abundance of wildlife species. Sixteen species of amphibians, fifteen species of reptiles, forty-three species of mammals, and two hundred forty-two species of birds have either been recorded or can reasonably be expected to be present on the refuge for at least a portion of the year. The wide array of both resident and migratory species found on the refuge is due to the varied habitat types found in the marsh/upland complex. The mix of wooded wetlands, emergent marsh, and mixed successional stages of vegetation on the upland areas all contribute to the species diversity of the wildlife community found at Montezuma.

The unique value of the refuge's habitats was officially recognized when Montezuma National Wildlife Refuge and the larger Montezuma Wetlands Complex were dedicated as New York State's first Important Bird Area (IBA) and a Globally Important Bird Area.

Montezuma plays a significant role in the Atlantic Flyway as a major staging, feeding and resting area for large numbers of migratory birds. An estimated one million birds pass through the Montezuma Wetlands Complex each year. In addition to waterfowl, numerous species of shorebirds, wading birds and neotropical migrants also depend on Montezuma's habitats.

Waterfowl A large proportion of the mid-Atlantic population of Canada geese utilizes Montezuma and the central Finger Lakes area during spring and fall migrations. Fall peaks of Canada geese routinely exceed 50,000 birds; in spring this number has exceeded 100,000. Approximately 15,000 snow geese use the refuge during spring migration. Tundra swans have often exceeded 400 in number during both spring and fall migrations. Late fall use by mallards has approached 100,000 birds. Use by American black ducks in the fall often exceeds 25,000.

Wood duck, gadwall, green-winged teal, American wigeon, northern pintail, northern shoveler, and blue-winged teal comprise the bulk of other dabbling duck species using the refuge during migration. Diving duck species that stop at Montezuma during migration include canvasback, redhead, ring-necked duck, and lesser scaup. Smaller numbers of bufflehead, ruddy duck, and common and hooded mergansers also utilize wetland habitats at the refuge during migration.

Overwintering of Canada geese in the Cayuga Lake Basin continued the trend of the last two decades. The numbers of geese staying in upstate New York has skyrocketed since the early 1970's. From overwintering populations of several hundred to a few thousand, current numbers annually exceed 100,000.

Marsh and Water Birds Several species of marsh and water birds may be found on refuge pools during the course of the year. The refuge's shallow pools, fringed by emergent vegetation, attract an abundance of great blue herons, green-backed herons, great egrets, black-crowned night-herons, Virginia rails, soras, American and least bitterns, common moorhens, and pied-billed grebes.

Several great blue herons nest on Maple Island in the Main Pool. The nests are located in live trees, and the dense leaf cover obscures the majority of the nests throughout the breeding season, making it impossible to determine how many of these nests were active and fledged young during the breeding season. Other marsh and water birds observed nesting on the refuge include black-crowned night herons, Virginia rail, sora, green-backed heron, pied-billed grebe, common moorhen, American coot, and American bittern.

Shorebirds Killdeer, spotted sandpiper, American woodcock, and common snipe are the only shorebird species that are common breeders on the refuge, although many other species are commonly observed during migration.

Mudflat and shallow water habitats at May's Point Pool and Benning Marsh during the late summer/early fall season provide excellent foraging habitat for migrant shorebirds. Virtually every species of shorebird that migrates through central New York was represented and recorded during the late summer and fall on May's Point Pool and Benning Marsh. Over twenty species of shorebirds were recorded on the two units. Rarer species observed included: Hudsonian godwit, western sandpiper, stilt sandpiper, Baird's sandpiper, buff-breasted sandpiper, American golden plover, black-bellied plover, and both red and Wilson's phalarope. Peregrine falcons and merlins were also observed on the pools, obviously attracted by the abundance of shorebirds. Montezuma has certainly become one of the most critical inland migratory stopover points for shorebirds in the eastern United States.

Black terns (a state listed endangered species) have recently returned to nesting in the wetlands of Montezuma. In the 1950's, the refuge saw peak black tern populations of 2,500 individuals. It is estimated that 500 young were produced in 1958. In the years that followed, black tern numbers declined to the point where no black tern nest were found on the refuge between 1987 and 1993. The decline is believed to be related to the invasion of purple loosestrife. Black terns nest in small loose colonies using floating masses of dead vegetation for nest sites. Purple loosestrife "chokes out" areas where a mix of emergent vegetation and open water once existed, creating monotypic stands of dense vegetation with low wildlife value. Additionally, dead stalks of purple loosestrife are rigid and resistant to decay, leaving no floating matter for use as nesting material.

It is of interest to note that the mix of shorebird species migrating through central New York is quite different from what is observed along the Atlantic Coast. Lesser yellowlegs, pectoral sandpipers, and Baird's sandpipers are much more common at Montezuma than at coastal resting areas. This is indicative of the extreme importance of Montezuma as a stopover site for birds that take an interior route on the southward migration.