The Jefferson River sport fishery is dominated by brown trout; rainbow trout are also present. Montana whitefish is an important native game species found in many rivers of western Montana. Westslope cutthroat trout are a species of special concern and are limited to six streams in the watershed. Montana arctic grayling is another species of special concern that is thought to inhabit the Jefferson River.
In recent years, the brown trout population of the watershed has declined. Montana Fish, Wildlife & Parks has estimated that the Jefferson can support a brown trout population of 600 fish two years or older per mile. Since the 1980s, the population has dropped below 200 brown trout per mile. During this time frame, several years of drought have occurred in the Jefferson resulting in increased stream temperatures and very low flows in the river during July and August.
Low flow conditions allow water temperatures to warm up. Warmer water means less oxygen is available to the fish. In addition, low flow conditions result in fish concentrating in deeper pools where they are more susceptible to prey including birds, other fish, mammals, and fishermen. Anglers should be aware that handling fish in warm conditions greatly increases the stress to the fish. Anglers can help trout cope better under these conditions by not fishing or fishing only at the coolest time of the day.
