During the 1600s and 1700s Lewiston was instrumental in the development of the Great Lakes region because it was the first drop off point for British and French traders, and goods shipped along the Niagara River. From Lewiston the goods were routed around Niagara Falls and transported south and west.

The original inhabitants of the area were the Seneca tribe, but they lost their rights to the land in 1763 at the conclusion of the French and Indian Wars. The Jay Treaty between Britain and the United States in 1796 set the border between Canada and America midway across the Niagara River. The site for a mile square village was chosen in the Mile Reserve area next to the river and named Lewis Town in honor of the governor, Morgan Lewis.

In the early to mid-1800s, Lewiston was the last stop for fleeing slaves from the South en route to freedom in Canada. Lewiston's citizens were great supporters of the anti-slavery movement and many volunteered to help smuggle thousands of slaves across the border. They lived by a code of silence and Lewistonians never trusted or spoke to outsiders about their secret activities.