The aquatic ecosystem is inextricably linked, through the riparian zone, with the terrestrial ecosystem. Species of fish in this stretch of the Snake River include rainbow trout (Salmo gairdneri), small-mouth bass (Micropterus dolomieui), chub (Couesius plumbeus), suckers (Catostomus spp.), and non-native carp (Cyprinus carpio). Sturgeon (Acipenser transmontanus), although once plentiful, are now rare.
Much of the Snake River and many of its reaches have been declared as critical habitat for the Snake River sockeye salmon (Oncorhynchus nerka), a federally listed endangered species, and the Snake River fall Chinook salmon (Oncorhynchus tschawytscha), a federally listed threatened species. In addition, the entire Snake River Basin has been designated as an Evolutionary Significant Unit for the West Coast steelhead (Oncorhynchus mykiss).
The Bull Trout (Salvelinus confluentus) from the Columbia River population within the Columbia River Basin is listed as threatened. The monument site lies adjacent to the Snake River, which is part of the tributary system of the Columbia River.