There are many endangered birds on these islands, including the Blakiston's fish owl, osprey, black stork, red-necked grebe, gyrfalcon, solitary snipe, Steller's sea eagle and the Siberian grouse.

[29] In the spring and summer, a number of seabird species nest on the islands, including black-headed and slaty-backed gull, common and thick-billed murre, horned and tufted puffin, spectacled guillemot, Aleutian tern, long-billed murrelet, and pelagic cormorant.

[30] The Kamchatka brown bear (Ursus arctos beringianus), sable and marten, caribou, red fox, and river otter are common on the Shantar Islands.

One of the most severe threats to the environment of the Shantar Islands is a proposed tidal hydroelectric power station, which is currently on hold for lack of funds.

[32] Lack of restrictions on tourism and resorting is also a problem as the number of people visiting the islands is increasing in recent years.