Here is a mid October trip...september the temps are warm, IMHO.

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Welcome to the BWCA...fall is gorgeous here...I encourage you to take the side trip...if coming from Oregon, IMO, I'd rent a boat

1)  skeeters are pretty much gone by end of Aug-early Sept
2)  fall colors vary, IMO...I think last week of Sept into 1st week of Oct are peak
3)  already been answered...there are plenty of campsites and little trouble finding one at that time of year

be prepared for variable weather.

Hiking or canoeing? Good question. My real destination is the Adirodacks in upstate N.Y., where I plan to spend a few days paddling, portaging, and camping in the canoe wilderness area near Mt.St.Regis. Then backpacking for a few days in the High Peaks area, including Mt.Marcy.
But Minnesota is sort of on the way from Oregon to N.Y., and the Boundary Waters Area sounds terrific. Mainly thinking of paddling, but haven't decided whether to bring my canoe all the way by car, or take the train and rent a car and canoe in N.Y. (in which case I'd have the same problem in Minnesota)

Is the question related to a hiking trip or a canoeing trip ?

If canoeing, you must use the designated campsites, though there is an exception for the Primitive Management Areas, which do not have designated sites.

I never thought about hiking in BWCA - are there enough designated sites away from the water trials for someone to go backpaking for a week or so ?   What about hunting season ?  What about that winter camping thread where people were talking about camping on the lake ice ?

I'd think that for hikers, there would be differnt rules, but maybe not.

Best to call the Forest Service and ask them for sure.

My favorite time of year....second week of september on....few/no bugs, fewer people, dynamic change.....

I was in Quetico the week after Labor day last year for 6 days. I think I counted about 10 mosquitos total.

Welcome aboard!

1) The mosquitos will be history after Labor Day.
2) Fall color peak is usually last week Sept-first week October.
3) In BWCAW you must camp at designated campsites (firegrate & latrine)
4) LNT is also law here.

:questions
I'm thinking about coming to the boundary waters in the fall. Can someone help me out - I've never been there, and am wondering about timing. 1) Are the mosquitoes, etc. pretty much gone by Labor Day?
2) When do the fall colors come in?
3) One other question - can you camp off-trail anywhere in the woods? Or do you have to find a wilderness campsite and stick to that? (In Oregon we're allowed to camp anywhere in state or federal forests, as long as we pack it out.)