The lagoon, which is also a State Game Refuge and a designated Wetland of International Importance, contains one of the largest eelgrass beds in the world. Thousands of waterfowl, including nearly the entire population of black brant, converge on the lagoon every fall from their nesting areas in Canada, Alaska, and the Soviet Union. The brant feed on eelgrass for up to eight weeks before their mass exodus, generally on a night in early November, to the Pacific Coast states and Baja California. Most of the birds fly non-stop to Baja in as little as 55 hours. Large numbers of emperor geese also pass through the Izembek Refuge.
Emperors breed in Siberia and Alaska and winter in the Aleutian Islands.
They begin arriving from the north in late August, and peak numbers occur in November and December. Also called beach geese, they feed on eelgrass in the lagoons and invertebrates and mussels on the beaches at low tide. Though most of the population pass through Izembek on their way to the Aleutians in the fall, many will stay on the Refuge until spring, unless a severe winter causes the lagoons and bays to freeze over. Tens of thousands of Taverners Canada geese also descend on Izembek Lagoon in the fall. Rarely, cackling Canada geese and Aleutian Canada geese are observed in the fall staging flocks of Taverner's Canada geese.