The Portneuf River originates upstream from Chesterfield Reservoir on the Fort Hall Indian Reservation and terminates in American Falls Reservoir. From American Falls Reservoir upstream to Pocatello, the river receives considerable spring water and contains populations of wild rainbow trout. The reach from Pocatello upstream to Marsh Creek contains very few trout, receives very little fishing pressure, and is severely impacted by sediment, irrigation withdrawals, damaged streambanks, and high water temperatures. From the confluence of Marsh Creek upstream to the Portneuf/Marsh Valley Canal diversion, silt conditions are less severe, but low flows caused by irrigation diversions adversely affect the populations of wild brown trout, the main game species in this area.
Conditions improve from the Portneuf/Marsh Valley diversion upstream to Lava Hot Springs. This area contains a mixture of hatchery and natural rainbow trout, brown trout, and cutthroat trout.
Major tributaries to the Portneuf River include Mink, Marsh, Rapid, Dempsey, Pebble, and Toponce creeks. They may serve as spawning areas for trout from the Portneuf River and nursery areas for fluvial trout; however, trout movement and the importance of these tributaries to the river is unknown.Four irrigation reservoirs are located in this drainage; Hawkins, Wiregrass, Chesterfield, and Twenty-four Mile. The lack of suitable spawning areas and annual irrigation drawdown precludes the development of any type of wild trout fisheries in these waters. Catchable and fingerling trout are released in spring and fall, respectively.