The Great Lakes were several large bodies of water that existed on Earth's North American continent along the border between the old nations of Canada and the United States of America. There were five Great Lakes in all, connected through various rivers to the Atlantic Ocean. (DS9: "Little Green Men")
On Miri's homeworld, which was an exact replica of Earth, a series of lakes identical to the Great Lakes could be seen on that planet's northern continent. (TOS: "Miri")
The Great Lakes are not mentioned in dialog but can clearly be seen on a United States wall map in "Little Green Men".