Fly Fishing Bozeman Mt. Outlook for September

August is now in the rearview mirror, and we “made it” through another unpredictable Montana summer. The year started off with a solid snowpack and plenty of moisture, but mid-March was unusually hot, and we lost a lot of low-elevation snowpack. Spring rains and snows saved the season as our runoff was slow and steady through late June. Overall, the summer has been solid on the big rivers in Southwest Montana like the Yellowstone and Madison.

• Cooler nights in September will rejuvenate rivers across the state with cold water and a return of hatching insects.
• This is brown trout pre-spawn season, during which they become increasingly active and aggressive through the month.
• Blue-winged olive mayfly hatches take center stage for dry fly anglers fishing the Yellowstone River, Paradise Valley spring creeks, and lower Madison River.

Top Bozeman Fly Fishing September Highlights

Upper Madison River

The upper Madison River has been a steady producer on our guided fly fishing trips throughout the entire season. The upper river, between Lyon’s and MacAtee has been our focus in the Madison Valley throughout most of August.

As the nights become longer and cooler, the sections between Varney Bridge and Ennis Lake will begin to fish well. Late September is an ideal time of year for experienced anglers who like to take a relaxed approach to the day, methodically working water while wading and floating the braided Madison River sections.

These days consist of streamer fishing while floating in between productive nymph-fishing runs where we typically pull the boats over and do some wading. The key is the weather – the best Madison River fly fishing of the month happens under overcast skies with mild temperatures and wind.

Lower Madison River

Warm water temperatures and heavy recreational traffic take the lower Madison River off of our radar for most of July and August. Conditions are now beginning to improve and traffic is quieting down – especially as cooler weather starts to settle across Southwest Montana in early fall. It’s still a morning game for now, but the fish have seen very few flies the last couple of months and simple dry/dropper rigs are effective setups to cover the deep runs and buckets in between Warm Springs and Greycliff.

Anglers fishing the lower Madison in September can expect prolific mid-day Pseudocleon hatches. These tiny mayflies are essentially blue-winged olives in sizes #20-26 and rarely inspire sizeable trout to surface feed. However, their nymphs are active and trout will become active during the pre-hatch hours, often selectively feeding on the miniscule nymphs.

This is an opportunity for anglers to practice their “match the hatch” skills, small nymphs like an olive tailwater tiny, little green machine, or micro-may are top guide flies in September on the Lower Madison River.

Streamer fishing becomes the mainstay later in September as the aquatic vegetation begins to dissipate. Brown trout become increasingly active during these pre-spawn weeks, aggressively chasing streamers as they move throughout the river system.

The entire river fishes well once things cool off by mid-month and our Bozeman fly fishing guides focus on the Warm Springs to Greycliff section. DIY anglers should consider fishing the Beartrap Canyon throughout the fall, either walking upstream from the canyon mouth near Warm Springs or downstream from the powerhouse below Ennis Dam. Nymph and streamer fishing is the way to go most days, but solid BWO mayfly hatches can show up when conditions align just right.

Yellowstone River

The longest free-flowing river in the lower 48 has been great so far in 2025, and September is typically one of the best times of year to fly fish the Yellowstone River. Cooler water gets aquatic insects moving around once again and the trout will begin to key into Hecuba and blue-winged olive mayflies as the month progresses. Experienced anglers fly fishing Paradise Valley can expect rising fish and solid hatches on cloudy days this fall.

The Livingston and lower river stretches are legendary for producing trophy brown trout in September and October. Streamer fishing is on serious anglers’ minds once the clouds roll in and the pressure drops with the first winter storms of the season. Whether floating and stripping big flies off the banks or swinging buggers through the deep holes, September is a time of year to aggressively prospect for big fish on the Yellowstone River from a drift boat.

Yellowstone River fly fishing trips tend to be a blend of floating and wading once water temperatures dip back into the low 50’s when the weather is right for it. Bright, sunny day tactics are a mix of nymph fishing and dry/dropper fly fishing riffles and drop-offs.

Overcast skies and mild temperatures bring ideal conditions this time of year. These are the days when BWO hatches are at their peaks and brown trout become more active in the shallow waters.

Other Regional Notes

The lower Gallatin, Jefferson, and Big Hole rivers are all running unusually low this season. Closures and restrictions will be lifted as water temperatures cool and fall progresses, but low flows will continue to be an issue for both anglers and trout throughout the fall of 2025.

Gallatin River fly fishing throughout the canyon sections between Big Sky and Gallatin Gateway picks back up as the days get shorter and nights cooler through fall. Longer shadows get trout feeling comfortable in shallow runs where they feed on nymphs and dries. Long leaders, fine tippets, and simple dry/dropper rigs are more productive than large attractor patterns in this low, clear water.

As September progresses, anglers can expect the overall fishing to improve on the rivers and streams near Bozeman. Dry fly anglers will note the fish begin to transition from opportunistically taking a mixed bag of terrestrial patterns to selectively feeding on hatch-matching flies. From the lower Yellowstone to the upper Madison River, this pattern is consistent across the legendary wild trout rivers surrounding Bozeman, Mt.

Bozeman Fly Fishing Guide Trips in September

Cloudy days that are accompanied by mild winds and temperatures are the highlight days when some of the biggest brown trout of the season end up in the nets of our guides. Anglers of all skill levels can expect productive days on the Madison and Yellowstone as the season transitions from summer to fall. This is a great time of the year for experienced anglers to target big fish using streamers while floating our big rivers.

Bozeman fly fishing trips can be booked online, via e-mail, or by calling us at 1-406-468-5019. Fins and Feathers Guide Service has been outfitting Montana fly fishing trips for 25 years. Join us this September to experience fall fishing in Montana with our expert guides.

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