Soaring in the sky, swimming through the waters, or roaming the land, the refuge protects a wide diversity of fish and wildlife species across the vast landscape of the Yukon-Kuskokwim Region.
The refuge supports one of the largest aggregations of water birds in the world. Over one million ducks and half a million geese breed here annually and in some summers, up to a third of the continent's northern pintails can be found on the refuge. In addition, nearly 40,000 loons, 40,000 grebes, 100,000 swans and 30,000 cranes return to the refuge each spring to nest. Millions of shorebirds use the refuge for both breeding and staging. In terms of both density and species diversity, the delta is the most important shorebird nesting area in the country, and the vast intertidal zone is the most important wetland for post-breeding shorebirds on the west coast of North America.
The refuge hosts approximately 80% of the continental breeding population of black brant and nearly all emperor geese. Cackling Canada and Pacific greater white-fronted geese number over 175,000 and 420,000, respectively. Undoubtedly, these four species have been a significant factor in shaping the coastal ecosystem.
Principal species of ducks that occur on the refuge include northern pintail, greater scaup, and wigeon. Harlequin ducks breed in many of the watersheds draining the Kuskokwim Mountains, as well as other suitable habitats. Common eiders are locally "common" in the vicinity of some brant colonies. The formerly abundant spectacled eiders have declined precipitously over the last 25 years.
Although Stellers eider nesting is nearly non-existent on the refuge, the adjacent waters are extremely important to a large fraction of this Pacific population. Tens of thousands stage each spring on Kuskokwim Shoals along the refuges southern coastline prior to moving to their arctic breeding grounds, and tens of thousands migrate south past Cape Romanzof in the fall. In addition, several thousand molt each fall on Kuskokwim Shoals and along the shoreline of Nunivak Island
Nineteen species of raptors have been recorded on the refuge, including golden eagles, bald eagles, and peregrine falcons. The Kisaralik River is among the most important areas on the refuge for nesting raptors, and supports one of the densest breeding populations of breeding golden eagles in North America.
Historically, caribou occurred on the Yukon-Kuskokwim Delta in large numbers and were the most abundant ungulate. Numbers peaked in the 1860's and during this period, caribou ranged over much of the refuge. Caribou subsequently disappeared from the region with the exception of small, remnant herds in the Kilbuck and Andreafsky Mountains. In recent years, up to 40,000 animals from the Mulchatna Caribou Herd have migrated onto the eastern portions of the refuge during the fall and winter period.
Bering Sea marine mammals add an interesting diversity to the refuge's wildlife and provide a vital subsistence resource for coastal villages. Pacific walruses, spotted seals, ringed seals, and Pacific bearded seals are hunted on the ice in spring, and some seal hunting continues during summer in bays and estuaries. Small numbers of threatened Stellers sea lions haul out on the rocks at Cape Romanzof and on Nunivak Island. Other marine mammals include harbor and Dall porpoises, northern fur and harbor seals, and beluga, gray, and minke whales.
Including the Bering Sea, refuge waters provide habitat for at least 40 species of fishes. The Yukon and Kuskokwim rivers, support regionally and internationally significant salmon fisheries. Other important freshwater resident species include several species of whitefish, sheefish, Alaska blackfish, burbot, northern pike, Dolly Varden, rainbow trout, and grayling. Nearshore ocean habitats harbor Pacific herring, halibut, tomcod and starry flounder.