During WWII, Submarines were built at Manitowoc Shipbuilding Company, in Manitowoc, Wisconsin and launched on Lake Michigan, then brought down the Mississippi River. That's the only instance I can think of for subs on the Great Lakes. read more
As others have suggested, the U.S. does not to my knowledge regularly use battleships or submarines in the Great Lakes. Most of the military vessels you would see on the lakes would be those of the Coast Guard. read more
Ive also read that from time too time the US Navy does in fact run training missions on some deisel subs throughout the Great Lakes as well. As far as Canadian subs operating in the Lakes there seems too be no mention whatsoever. read more
Niagara Falls — Divers from the U.S coast guard took part this morning, in a delicate wreck recovery operation to bring to the surface a Nazi submarine discovered two weeks ago at the bottom of Lake Ontario. read more