Salmon returns to natal streams fuel this coastal ecosystem during the summer and fall. This rich fishery provides quality forage for coastal brown bears and other predators. The Southern Alaska Peninsula Caribou Herd (5,400 animals in 2002) also inhabits the Refuge. Several species of marine mammals either inhabit or pass through Refuge coastal waters and lagoons. These include harbor seal, sea otter, walrus, the threatened Stellar's sea lion, and gray, minke, killer and humpback whales.

At the heart of the Refuge is the 150-square mile Izembek Lagoon. The lagoon and its associated state-owned tidal lands have been protected by the State of Alaska since 1960 as the Izembek State Game Refuge. Here, shallow, brackish water covers one of the world's largest beds of eelgrass, creating a rich feeding and resting area for hundreds of thousands of waterfowl. Virtually the entire population of Pacific black brant (150,000 birds on average), Taverner's Canada goose (55,000), and emperor goose (6,000) inhabit the lagoon each fall. Approximately 23,000 threatened Steller's eiders also molt, rest, and feed at Izembek each autumn.