Fish species on the Alagnak include king salmon, silver salmon, red salmon, chum salmon, rainbow trout, char, grayling, northern pike, Aleutian sculpin, slimy sculpin, Alaska blackfish, three spine stickleback, Japanese lamprey, round whitefish, and nine spine stickleback.
Sport fishing, commercial fishing, and subsistence fishing all occur on the Alagnak. All types of fishing are reliant upon the success of the salmon life cycle. The life cycle of salmon vividly expresses the significance of one element within an ecosystem.
The large salmon runs in Bristol Bay are subject to a carefully managed commercial harvest prior to their arrival in individual rivers including the Alagnak. The Alaska Department of Fish and Game allows commercial fishing only when there are enough fish to meet sufficient population numbers for spawning populations, subsistence, and sport fishing. The Alagnak's extraordinary rainbow trout, char, grayling, and abundant salmon are some of the most attractive sport fish in the world, and the river has become the most popular fly-in fishing location in all of southwest Alaska. Although the fishing is exceptional, these prized sports fish are still vulnerable to overfishing. The Alaska Department of Fish and Game carefully monitors the populations to ensure that the present regulations maintain the long-term stability of the Alagnak sport fishery. Subsistence fishing on the Alagnak is for local rural residents only. During the summer camps are set up on the river and fish are gathered for smoking, salting, canning and freezing. Salmon harvested in the summer is the primary food source for subsistence users year round.