The Alagnak Wild River is inhabited by a wide diversity of species typical of southwest Alaska. The Alagnak provides critical bear habitat during the summer and fall; large populations of brown bears feed on salmon that spawn in the river.
Moose are attracted to riparian habitat along the Alagnak throughout the year. The drainages west of Kukaklek and Nonvianuk Lakes provide winter habitat for caribou. Furbearers found along the river include beaver, lynx, mink, otter, fox, wolverine, and occasionally wolf.
Salmon are among the Alagnak River's most significant resources and an important reason for its designation as a Wild River. The Alagnak flows into the Kvichak River, and ultimately Bristol Bay, which is one of the largest and richest commercial salmon fisheries in the world, with sockeye salmon the most abundant species taken.
Biological inventories have been completed for birds, mammals, fish, vascular plants, and soils. Because of its remote location and limited access, monitoring activities in Alagnak have been limited and instead take place in neighboring Katmai National Park and Preserve.