The western portion of the park area is bisected by the Snake and Clearwater rivers and many of their reaches. Many of these drainages have been declared critical habitat for the Snake River sockeye salmon (Oncorhynchus nerka)and the Snake River fall chinook salmon (Oncorhynchus tschawytscha), in addition to being important habitat for the West Coast steelhead (Oncorhynchus mykiss) and brown trout (Salmo trutta).
Historically, in late May and early June, the rivers filled with eels, steelhead, and chinook salmon. The aboriginal Nez Perce villagers crowded to communal fishing sites to trap the fish, or haul in fish with large dip nets. The first fishing of the season was accompanied by prescribed rituals and a ceremonial feast known as kooyit. Thanksgiving was offered to the Creator and to the fish for having returned and given themselves to the people as food. In this way, it was hoped that the fish would return the next year.