[2023] Guide to Jefferson River Fly Fishing

Southwest Montana is undoubtedly home to some of Montana’s best fisheries. It is famous for its views, the small-town vibe, agriculture, fly fishing, and the wonderful valley itself. Recently, the Jefferson Valley and its fishery have become increasingly popular, gaining recognition from its years of being overlooked.

Up top, the Beaverhead River, Ruby River, and the Big Hole river meet at the confluence to form the Jefferson or the “Jeff.” With the convergence of the Big Hole and Beaverhead in Twin Bridges, Montana, the Jefferson is a large stream with many braids. The Jeff, Madison, and the Gallatin will all combine at Three Forks, Montana to form the Missouri River further downstream.

The Jefferson, over the years, has struggled with trout numbers and dewatering. However, work has been and continues to be done to improve the river’s fishery so its numbers can be enhanced and compete with its nearby river’s trout populations. In 1988, the drought had the river so low that pools were formed with zero flow in some locations. The process of how much water and where it is diverted into the valley’s canals for agricultural purposes is vital. Since 1988, a drought management plan has been in place to keep irrigators’ flows at specific cubic feet per second, around 50 CFS during the irrigation season. This plan has helped ensure that even on low water years, there won’t be pools or closures again on the Jeff.

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When to Fly Fish the Jefferson River

The Jefferson River is open year-round but flies fishing is best from April to October. Our favorite times of the year for Jefferson River fly fishing are late spring, just before the runoff, and just after the runoff in early summer. There is reliable fishing throughout the summer months as well, but conditions vary from year to year depending on weather patterns and winter snowpack. The river typically fills with aquatic vegetation in low summer flows, so it can be difficult to fish with anything other than a big dry fly by early August. The Jefferson can be tough to beat in October and early November if you want a big Brown Trout and like to fish big streamers.

Highlights of Jefferson River Fly Fishing

Early season, as the water flows are dropping and clearing following the runoff, is our favorite time of year to fly fish the Jefferson River. Oftentimes, when there is only a foot or two of visibility, and the waters are still above the “summer” bank, Jefferson can fish as well as any river in the west. Big streamers and nymphs fished on heavy tippet right against the bank from a drift boat can be deadly on the big browns that are normally very wary the rest of the year. Good flows this time of year give the normally placid river a lot of character in higher flows and always make for a great time on the water.

Hopper fishing on Jefferson can be “hit or miss” during July and August but is something we like to try every few days with experienced anglers. It’s pretty typical to go away between fish this time of year as lower summer flows tend to concentrate the trout into smaller areas of good holding water. However, the trout that do come up to eat a hopper often do so with authority, run hard, and average in size around 16+”.

Tricos are small, black mayflies that hatch in the pre-dawn hours and then come to the water surface late morning in what is described as a “spinner fall.” These hatches are very dense, with the spinner fall being the kind of experience you must see to believe. The vast numbers of bugs that end up on the water bring trout to the surface in the late morning and can provide some great “match the hatch” dry fly fishing where we target specific trout as they slowly sip down the spinners.

Sections of the Jefferson River

Twin Bridges to Cardwell
The Jefferson River is a large river that runs through a gorgeous valley. There are three distinct, long sections that the river consists of. The Jeff begins near the fishy farm town of Twin Bridges, Montana. The neighboring Beaverhead, Ruby, and Big Hole rivers meet to make the Jefferson right outside of town. From the confluence of the upper section, the river flows, bends, and meanders for fifty miles through the arid Jefferson valley, a must-see. A backdrop of the Tobacco Root Mountains while floating on this section paints unforgettable pictures. The river flows at a consistent pace, flat with braids and side channels. No rapids or rough water describe the upper section, but there is the occasional sweeper tree to look out for. Many great undercut banks, long runs, and deep wavetrain riffles in this section hold some lurking, large trout. The bushy banks with cottonwood backdrops keep the angler intrigued with constant targets to cast at. These targets tend to have the shallow, large brown looking for some giant bugs. Large dry flies and streamers make the upper section one of the most during the season’s peak. The end of this fifty-mile section ends in the town of Cardwell.

Jefferson River Canyon
In the middle section, the Jefferson River leaves the flat terrain and flows downward into a canyon. The Jefferson Canyon Below Cardwell, the Jefferson cuts directly through the Tobacco Root Mountains, providing some incredible geological views. A road on one side parallels the river while railroad tracks follow it on the other. For the walk and wade angler, this can be a solid opportunity for access. With rocky canyon walls, the river flows a bit slower and more profoundly. Stonefly hatches early into the post-runoff season in the rocks can get the fish-eating good. Fishing deep nymph rigs with a pat’s rubber leg or a golden stonefly chubby Chernobyl with a long dropper and heavy nymph can be a great bet in the canyon.

Jefferson River Canyon to Three Forks
The lower section of the Jefferson River emerges from the canyon and flows into another wide, open valley. In this section, the river gets broken up into many braids and channels. This can be great for the walk and wade angler, as the canyon section. Walking these small channels can be a lot of work as the trout numbers can decrease lower, but great rewards are large. The Cottonwood trees line the bank, while hay fields hold a significant number of hoppers. On good water years, this lower section can fish well during terrestrials.

Seasons on the Jefferson

The Jeff is extremely condition-dependent as it is a large river, lower in the valley. As a result, its season is short-lived. The neighboring Madison, Big Hole, and Beaverhead are blue-ribbon streams that can fish year-round where the Jeff has its windows. Starting in the spring before snowmelt and runoff, the Jeff can fish wonderfully since the trout population is not at large, the fish that around lurk lonely and have some significant size. Large brown trout thrive in Jeff’s given structure with gravel bars, fallen trees, and undercut banks, looking for big meals. Covering water is critical. Floating with a boat and fishing streamers is one of the best ways to fish the Jeff productively.

Spring
In Southwest Montana, runoff typically comes in hot in May, making the great wait to fish it again in late June or early July. Runoff murks the water up, but it is game on to start looking for those big fish when it clears. The river holds a solid stonefly population; golden stoneflies are a popular post-runoff pattern. Big foam Attractor dry flies can leave the willing fish with no choice but to come up. Dropping off big attractor nymphs like worms and rubber legs deep in those undercut banks and riffle drop-offs can turn a harsh, dry fly bite into productive fishing. It is known for the Jefferson to fish the best on dark, stormy or cloudy days as it puts those larger fish on the prowl. When covering water looking for few but nice fish, this is a crucial factor in having a good or great day. Cloud cover on the Jeff can bring on unexpected Caddis hatches and get those lurking fish to feel more comfortable to get up on the surface.

Summer
As the summer season progresses, water levels drop, and temperatures increase. The landscape and terrain in the valley are perfect for hoppers. For large trout, they can’t resist a high-protein meal that a grasshopper offers. Take advantage of a warm, 5-10mph windy day blowing these bugs onto the bank, and it can get fun quickly. Taking the boat into side channels or even finding smaller braids to wade, for that matter, can make for some fun hopper fishing on the grassy, undercut banks. Getting out on the water early in the morning can be a gamechanger with the warmer temperatures in the heat of the day during the dog days of summer. Early Fall can still be hot; during late August and early September, temperatures can reach dangerous levels for the sake of the thriving trout. Make sure proper trout handling is taken into care and, again, fishing during the cooler times of the day.

Fall
As fall approaches and the temperatures begin to drop, the fish get happy again. Streamer fishing can be incredible on the Jeff during the Fall. Both numbers and trophy-sized fish are found during the Fall.

Jefferson River Flies

Dry Flies:

Chubby Chernobyl (size 4-14)
Amy’s Ant (size 10-14)
X Caddis (size 8-18)
Sparkle Duns (size 12-20)
Turk’s Tarantula (size 6-14)
Pink/Black Morrish Hopper (size 8-12)
Parachute Hopper (size 8-10)
Sweetgrass Hopper (size 8-12)

Nymphs

Two Bit Hooker (size 12-18)
Pat’s Rubber Legs (size 6-14)
Red Copper John (size 12-18)
Zebra Midge (size 14-18)

Streamers

Barely Legal – olive/white (size 4)
Home Invader – black, white, olive, yellow (size 6)
Bow River Bugger (size 4-6)
Sparkle Minnow Sculpin (size 4-8)

Lodging Options

Four Rivers Fishing Co – Located in Twin Bridges, Montana, Four Rivers Fishing Company is one of the oldest full-service fly fishing operations in the area. With five of Montana’s most famous rivers located within a 40-mile radius of Twin, this is truly the “trout Mecca” of the lower-48. Four Rivers is licensed to outfit on every watershed in the region, and on a daily basis guides the Big Hole, Beaverhead, Madison, Jefferson, and Ruby Rivers. Four Rivers claims to have one of the best guide staffs in the region, and their combined number of seasons attests to that. To complement their outfitting offerings, Four Rivers’ lodging program is extremely flexible and varied. They also offer their clients numerous dining options, including various steak houses and restaurants in and close to town (a fun alternative and complement to the typical “lodge-style” meal program). Collectively, Four Rivers offers a great fishing and lodging package with some of the best prices found anywhere in the Northern Rockies.

Ruby Springs Lodge – Ruby Springs Lodge has a well-earned reputation for being one of the best-run, most exceptional fishing lodges in the entire Western United States. High-end and incredibly nice in every detail, this operation consists of two main lodge buildings and a number of private cabins built directly on the banks of Southwest Montana’s Ruby River. The cabins are truly magnificent and the amenities and setting will satisfy even the most discriminating guests. The numerous meandering miles of the Ruby River and Clear Creek – the lodge’s “home waters” – provide guests access to a private and intimate fishery that is unpressured and loaded with fish. Fish the lodge’s home waters and then spend a day or two floating a few of Montana’s famed rivers, all located within a close and easy drive from the Lodge. A Ruby River fly fishing experience should be on every trout angler’s fly fishing bucket list.

Stonefly Lodge & Inn – The Stonefly Lodge and the Stonefly Inn – an operation that calls itself “Montana’s Last Best Fly Fishing Lodge” – is located in the heart of Montana’s “Blue Ribbon” trout country. Based out of Twin Bridges, the Stonefly Lodge & Inn giving angling guests opportunities to fish famous Southwest Montana rivers such as the Big Hole, Beaverhead, Madison, Jefferson, and Ruby Rivers. With some of the finest guides in the state, this operation offers more than three hundred miles of world-class Montana fly fishing water, all within a one-hour drive of your door. With five “Blue Ribbon “ rivers, choice of accommodations, and the best guides in the zip code, the Stonefly Lodge & Inn is one of Yellow Dog’s favorites. Low-key, relaxed, and comfortable, this is one of the very best destinations in the region.

Other Nearby Rivers:

– The Yellowstone River
– Madison River
– Gallatin River

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