You can rent a canoe on Lake Louise and Emerald Lake.  (Moraine Lake canoes and rowboats are now apparently reserved for Moraine Lake Lodge guests' use.) Blue Canoe rents canoes and kayaks at their dock on the Bow River in the Banff townsite.

Motorized boats are only allowed on Lake Minnewanka; there, you can rent an aluminum fishing boat to fish or just explore. Pedal boats are also available.

You can also cruise Lake Minnewanka in a boat tour.

Parks Canada has an excellent resource on canoeing the Bow River, which includes safety information on canoeing in Banff National Park as well as detailed route information for the Bow River.