During the spring and summer months, the secondary dunes and the swale complex display an impressive array of wild flowers, grasses, and orchids, including: Deptford pink, horseweed, wild indigo, false heather, red fescue, Marsh Straw Sedge, Path Rush, peppergrass, poor-man's pepper, wild carrot, hyssop-leaved thoroughwort, common highbush blueberry, large cranberry, rose pogonia, snake mouth orchid, calopogon, grass pink orchid, silver rod, indian grass, sickle-leaved golden aster, mountain sandwort, ox-eye daisy, goldenrod, butter and eggs, toadflax, slender fragrant goldenrod, blue-eyed grass, cinquefoil, rose, round-leaved thoroughwort, tall wormwood, wood/common strawberry, common evening primrose, and beach pea.

Wetlands Two wetlands of approximately one acre each in size occur within the dune/swale terrain. Dominant plants are common threesquare and rush. Phragmites, an exotic and invasive plant, is scattered throughout these wetlands, and cranberry is sometimes found near the shallow fringes.

Fish and Wildlife The coastal location of the refuge serves as an important migratory route for a variety of species including shorebirds, songbirds, and raptors. Ipswich sparrows, a race of the Savannah sparrow, are known to winter at the refuge. The refuge serves as a foraging area for piping plovers, least terns, common terns, roseate terns, and royal terns. Piping plovers and least terns also nest on the refuge. A number of secondary dune species, which are in decline on Long Island, use this refuge, including eastern hognose snake and eastern spadefoot toad.

Raptors--The refuge provides important grounds for raptors migrating along the coast. American kestrels, merlins, peregrine falcons, sharp-shinned hawks, and Cooper's hawks have been documented at Amagansett during migration. Up to 100 American kestrels in one hour have been observed during the peak of autumn passage. Snowy owls and rough-legged hawks have also been documented during the winter months.

Waterfowl--Waterfowl primarily use offshore areas. During the winter months, sea ducks and diving ducks may be observed. The most common waterfowl species observed in the area include white-winged scoter, surf scoter, long-tailed duck, and red-breasted merganser.

Shorebirds, Gulls, Terns and Allied Species--The marine beach and swales provide habitats for a variety of sandpipers, plovers, gulls, and terns.

Herring gull, great black-backed gull, and ring-billed gull are common year-round at Amagansett and northern gannets can be frequently observed from the refuge's beach in winter. Black-bellied plovers and sanderlings are the most common shorebirds using the beach.

Other Migratory Birds--Breeding and wintering songbirds use the undisturbed grass/shrub habitats of the refuge. Ipswich sparrows have been documented in winter on the refuge and on adjacent lands. A total of 26 migratory bird species has been documented at Amagansett NWR. The most common species observed on the refuge include the rufous-sided towhee, northern mockingbird, America robin, mourning dove, common grackle, common yellowthroat, prairie warbler, song sparrow, red-winged blackbird, northern bobwhite quail, field sparrow, and tree swallow.

Reptiles and Amphibians--Refuge staff periodically observe eastern hognose snakes at Amagansett. The hognose, once abundant on Long Island beaches has been steadily declining in numbers.

Rare, Threatened and Endangered Species--The federally endangered roseate tern uses the beach at Amagansett NWR as a resting area and forages in offshore waters. Piping plovers, a federally listed threatened species, also forage and nest at the refuge. Like roseate terns, New York State threatened least terns use the beach as a resting and nesting area. New York's Natural Heritage program lists records of the state endangered round-leaf boneset and threatened little-leaf tick-trefoil at Amagansett.