I grew up in the Great Lakes and remember how chilly it can be there, even on summer nights. In the Boundary Waters, hypothermia is going to be your number one concern, no matter the season.
Planning and preparation are paramount. Dress properly, as clothes are your primary shelter system. Avoid wearing anything that is 100 percent cottonlike jeansand consider wearing wool or poly/cotton blends.
If you're stranded, I'm going to assume that you filed a travel plan when you obtained your permit. Stay put and wait for help. Hopefully, you can flag another canoe party. If not, then you could have a long wait ahead before searchers realize you are overdue. Hunker down and focus on your immediate survival priorities.
In that region, this means constructing a makeshift shelter like a lean-to that will keep out the rain and wind. Then make a fire (assuming it is a safe time of year to do so). It is absolutely critical that you carry some survival items in your pockets at all times. That fancy survival kit in you canoe or backpack wont do you much good if you become separated from it.
When I head out on canoe trips, I always carry three firestarters in my pockets, signal mirror, pocketknife, Iodine tablets, and a Heat-Sheet Blanket. These weigh ounces, but are life insurance should you become lost.
Finding water shouldn't be much of a problem, eh. Boil it for one minute to purify, or use the Iodine from your survival kit. Most hypothermia and frostbite victims suffer from dehydration so tank up on water.
Lastly, when traveling in such a rugged landscape, I highly recommend investing in a Personal Location Beacon (PLB). This device can direct Search & Rescue personnel right to you.