Beginning Monday, a five-day, around-the-clock operation will begin in 300 feet of water about nine miles off the shore of Hamilton, Ontario, which is on the western end of Lake Ontario.
Some 50 sailors' remains are believed still aboard the wrecks of the 60-foot Scourge and the 50-foot Hamilton, the Canwest News Service reported.
Experts from Parks Canada, the Canadian navy and Coast Guard, independent archaeologists, provincial, municipal and U.S. governments are taking part in the exploration.
Project coordinator Ian Kerr-Wilson said there were no plans to bring the ships up, as the U.S. Navy considers them to be maritime grave sites. He told the news agency any images of remains would also not be made public.
The ships were part of the War of 1812 assault on British forces in the city of York, now called Toronto.