I'm looking at going on a trip in mid September and I'm wondering if there is much of a difference compared to going in June like I'm used to. I've gone in August once before too so I don't think it will be too radically different.

The differences I'm looking at are bugs, traffic and temps. I don't expect it to cool down that early but this is Minnesota so who knows. Is it the flies that are the biggest issue that time of year? For traffic, I'm looking at the east side. Is there a notable difference in traffic between June and September?

Traffic over much of the BWCA takes a big dip after Labor Day weekend.

Bugs tend to only be annoying in the early morning and late evening for an hour or so, depending on the temps. It could be very warm still, or could be getting chilly at night. Rain will affect the bugs as well. All in all, I like going in mid-May and early to mid September. Usually cooler temps, less bugs, less traffic.

Most important difference is the length of daylight. Much less ambient sound. Loons are subdued, few insects, few frogs, limited birdsong.

Lots of good info so far. Here is a link to the Sawbill Outfitters weather history... it will give you a good idea of Sept temps Sawbill weather history
I'd still throw in to small container of bug repellant though, just to be safe...

In Sept. all those things will have declined. The later in Sept. it is the more true that is. The first week or so, may still be a few bugs around in the evening. Take a headnet, insect shield buff, a little bottle of repellent. After the Labor Day week, there'll be fewer people; if it's a nice weather weekend, there'll be more, but mostly concentrated not too far from the entries. Average temps will be moderate - 60/65, 45/40 - but record highs and lows can differ by 20 degrees. The weather will be more variable/changeable than earlier, windier. Daylight is fading to shorter and shorter days - 13 hours or so.

With good timing you can return to join the Fall wingnight gathering.

I love tripping in September for the reasons stated, It can, however, be the best of times or the worst of times depending on the weather. Late September can be absolutely beautiful. It can also be wet, windy and cold. But the bugs are not a factor and you get to enjoy campfires more due to the shorter days, all with fewer folks around.
June or September? September for me in a heartbeat.

Banksiana: "Most important difference is the length of daylight. Much less ambient sound. Loons are subdued, few insects, few frogs, limited birdsong."

The shortened daylight is the most noticeable thing IMO. It's actually dark at 6-7am (relatively) and gets dark by 6:30-7pm. But the other thing is lack of bugs. I had basically no mosquitoes from Sept 8 to 13 last year (or any other bugs to speak of). It was amazing. Less wind than June too. I really enjoyed that time of year. Trees were just starting to turn... if you wanna catch fall colors, go a week later. Even less daylight but also even less bugs. :) I recommend a route with a lot of elevation so you can see all of the trees changing.

I like to go the week after Labor Day for all of the reasons given above. It's generally been a good trip weather wise and bugs. Also like that it get's dark a bit earlier.

September is a great month! My 40 day trip brought me to September 28th. I got wind bound on Lac La Croix about a week from the end and the morning the wind died enough it was about 18 degrees. Had frost in the morning quite a bit the last two weeks. Same campsite in May and September on Iron I had last frost in spring and first in fall of that year. Haha. Bugs are a rarety most the time for me. Light was a concern... but I liked getting up and doing coffee before light. All part of the adventure. I was surprised how many people I saw. Enjoy... you’ll love it!

There could be a big range of temps, especially from early Sept. to late Sept. I have paddled in the BWCA the last 4 Septembers, all between the 11th and the 20th. The high has been 70°F, the low has been 34°F. The average high has been around 55°F, the lows generally around 40°F. During this time period the bugs have been non-existent. I wouldn't plan on swimming. It's my favorite time to paddle and camp.

My trips are in early to mid September. Unless you camp near a stagnant water area you won't see many bugs. But in 2017 on a solo I was overun by mosquitos at two different sites. The early dusk has me listening to the CBC on headphones or reading by headlamp in the hammock.

Woke up one morning second week of September to 28 degrees at Upper Basswood Falls. Perfect. The walleye fishing at Wheelbarrow Falls was outstanding. Great time to go.

Dodger.

Compared to June: Roughly same temps, less people, less bugs.

mid Sept is the very best time (IMO).

Less:
Mosquitoes
People
Black Flies
Heat
Wind

More:
Yellow jackets :-(