The Village of Waddington is at the northern edge of the town and is north of Canton.
The first settlers arrived around 1798.
The village was originally called "Hamilton" (after Alexander Hamilton), but was changed to Waddington in 1818. Joshua Waddington was a friend of Hamilton and one of the original landowners. The village was incorporated in 1839. When the Town of Waddington was formed afterwards, it adopted the name of the village.
During the construction of the St. Lawrence Seaway part of the village needed to be relocated and some of the old industrial area was destroyed.