The Town of Watertown is located in the central part of the county. Part of the City of Watertown borders the town.
Numerous sites of the aboriginal habitation were found by early surveyors of this region. The region was later part of Macomb's Purchase.
Watertown was established as a town in 1800 before the formation of Jefferson County, while still in Oneida County, New York. The Towns of Rutland, New York (1802) and Hounsfield, New York (1806) were soon formed from part of Watertown.
The town was first settled in 1800 around the time of the first permanent US military presence in the region, which was established at nearby Sackets Harbor to guard the international border and to fight smuggling in the St. Lawrence region.
In 1816, the community of Watertown set itself off from the town by incorporating as a village. It became a city in 1869.