Lake of the Woods and Area
At 1,000,000 acres and 14,522 islands, Lake of the Woods is one giant canoe route. You could paddle the lake the entire summer and only see parts of it - it is that big! In addition to the lake itself, several adjoining routes run up the Winnipeg River and east toward Dogtooth, Kilvert, and other lakes.
If you are a novice canoeist, this area, while rugged, is probably a good choice. You can increase your confidence by using the services of a canoe outfitter, of course.
Just east of Lake of the Woods is Kakagi (Crow) Lake, one of the most picturesque and beautiful lakes in Sunset Country. Paddlers have many options in Kakagi's crystal-clear waters and adjoining waterways.
Eagle Lake -Vermilion Bay/Dryden Area
Many routes here are relatively short compared to others, making this an excellent area for less experienced canoeists. Options include Eagle Lake, Hawkcliff Lake, Populus Lake, and Dogpaw Lake, which take you through Upper Wabigoon Lake and the English River, among others. The fishing opportunities are out of this world. Check for what's available here.
Wabakimi
As one of the largest Provincial Parks in Ontario, Wabakimi is another bucket-list destination for any serious paddler. Because the Park is so large, you can choose from various routes.
Wabakimi is rugged and remote, so we recommend hiring an outfitter for your trip. Several offer established packages to consider. Areas with routes adjacent to Wabakimi include those in Kopka River, Albany River, and Brightsand River Provincial Parks.
More Info: Wabakimi Canoe Outfitters
We recently worked with Destination Ontario and brought in Colin Field, who wrote an article about his adventures in the park. See that article here.

Canoeing.com has a guide about paddling in the park, which you can read here.