Watertown is a city in Dodge and Jefferson counties in the U.S. state of Wisconsin. Most of the city's population is in Jefferson County. Divisiā¦Watertown is a city in Dodge and Jefferson counties in the U.S. state of Wisconsin. Most of the city's population is in Jefferson County. Division Street, several blocks north of downtown, marks the county line. The population of Watertown was 22,926 at the 2020 census. Of this, 14,674 were in Jefferson County, and 8,252 were in Dodge County. Watertown is the most populous city in the Watertown-Fort Atkinson micropolitan area, which also includes Johnson Creek and Jefferson.