I checked and the invention or at least the widespread implementation of lock systems didn’t occur until well after this conflict. How, then, were these bodies of water useful to the British?
If you wanted to travel by boat from one lake to another did you do that without the proper infrastructure? Like pick up your boat/canoe/whatever and just go home?
There's always more to be said, but you may find more info in this post by u/PartyMoses about the method of travelling overland between bodies of water known as portage.
The indigenous peoples and French voyageurs used this method to navigate the breadth of the Great Lakes water basin in order to obtain and trade furs and goods for centuries. You would have to leave the body of water, carry your canoe, goods and supplies and travel overland until you reached another river or lake, then continue your journey again by water. Canoes were light and surprisingly portable too.
By 1812, the British had already built some roads in the Canadas between settlements, though much of the colony's terrain was still rugged at the time. These would also be used during the war by the British, if lake travel was not safe or possible -- such as after the Battle of York in 1813, when the US briefly captured the town. The British had to withdraw overland to Kingston.
Various rapids and Niagara Falls continued to be natural obstacles for both sides, until the construction of canals years later, which allowed vessels to bypass these hazards.