Try these guys. Been there twice and wouldn't even think about using anyone else for SW Montana.
http://www.thestoneflyinn.com/
Montana should be great in September. I just got back from 2 weeks fishing in Ennis,Dillon, and Livingston. The rivers have a lot of water, and the fishing was the worst I have seen in 25 years because the fish are spread out and the bugs cycles are off. Things are 3-4 weeks late. So you should have good water levels and probably hoppers in Sept.
Where you go depends on how much money you want to spend on quides to float certain rivers. For wade fishing, it is tough to beat West Yellowstone, and I second the advise about Blue Ribbon Flies for quidance.
The Dillon -Beaverhead,Big Hole,Jeffrson- area (use Frontier Anglers) and Craig (Missouri River Lodge) are best fished floating. Wade fishing is possible, but more limited than West Yellowstone. The Ruby is the exception, but the big fish options require a boat. The spring creeks in Livingston are an option but cost $100-125/day to fish.
Missoula has the Bitterroot and Rock Creek (a terrific stream) for wade fishing and the Clark Fork and Blackfoot (beautiful float, but spotty fishing) for floats.
Lots of options, and it should all be good this year
What does Southeast Montana have in the way of Fly Fishing?
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