I've done three September trips.  You can check out the trip reports here (You need to Login or Register to view media files and links) and get an idea of what I encountered.  In sum - as has been noted - expect everything from freezing to hot, from clear skies to rain and wind.  But you don't have to worry about finding campsites because the place is much less populated (generally speaking).  In any case, no matter when you go, you should be at your campsite by 2:00 pm - in the summer because there's often competition, and in the spring and fall because you don't have as much time to set up.

One other thing not mentioned is the fishing.  I do a trip the first week of June and one mid-September every summer.  First week of June is usually great walleye fishing.  September is hit or miss for the walleye.  They may still be 20 feet or they may be 5 feet in the evening.  September, bass and northern are usually very aggressive unless you get one of those early season snows and that usually shuts things down for a day or two.  Just my past experiences.  But agree with rest, especially about the weather.

Imagine Soft Silent Leaf 

Imagine Sincere Solitude

Imagine Gold Fall Trees

Imagine Gratitude

Imagine Soft Still Speak

K

I would only emphasize that mid-September is a time when you want to make double-sure your gear (and you) are ready for whatever weather you may get. For example, it's no time for a tent that's past its prime or has never been tested in strong winds or downpours (personal experience). An extra fly and some extra warm clothes like fleece jackets/stocking caps in a dry bag may prove well worth the extra weight. Finally I'd suggest you take along some lightweight long-johns. (I like "Wickers.")  --Goose

All of the above is great advice.
I like cool/cold evenings for the fireside ambiance and great sleeping.

Would rather have to unzip a sleeping bag, than add layers of clothes.

Early May trips and late season trips are were Dri-Fly type tarps really shine.

Sitting under that 3-sided tarp with the warmth from your campfire reflecting inside makes even the worse weather tolerable.

Leaves will just be starting to turn, but if you go end of Sept, you'll have max color.  Chicken's post is correct, bring warmer bags.  Over the last decade, I've had snow to 80 degrees (this last year).

I have taken one early September trip, and loved it. The crowds were less, the weather for the most part was mild. The one thing that struck was me was the weather contrast. On a 9 day trip the first half was warm, a "typical" summer weather for a trip. The second half was again warm during the day but at night temperatures plunged slightly and I regretted leaving my 15 degree sleeping bag at home.

I second everything Solus said about tripping in September.

IMHO, the most important thing to keep in mind when planning your trip: the days are shorter - it gets dark earlier so, obviously, you need to get off the water earlier.

As for weather, we've experienced mid-summer temperatures (two years ago) and we've experienced sleet and high winds (last year) so weather is very changeable.

Water levels are usually at their lowest for the year so wet portages are often dry and paddable water often must be portaged.

Most outfitters are still operating but it is definitely a good idea to call ahead and let them know when you'll be arriving.

Have a great trip!

Leaves will be turning. Could be warm, could be cold- often a bit windy. Bugs are light to none, people are less, days are much shorter (bring good light). Fall is a wonderful time to trip.

Hi all, looking at planning a different trip this year. Usually, my group has gone to canoe country in early to mid-June, but this year schedules are dictating that we go in mid-September instead.

I am guessing that at that time of year weather will be a bit of a crapshoot (much like our June trip--we are ready for nearly anything), but I was wondering specifically about any other thoughts anyone would have about differences between the two times. I am thinking that not as many visitors would be in the park then (I am thinking Sept. 15th or so), is that right? Bugs should be on the way down correct? Will leaves be starting to turn then? Are most outfitters still rolling along then fully open?