- Your Ad Here Seneca County is a county located in the U.S. state of New York. As of the 2016 census, the population was 34,777. Two villages share the duty as the county seats: Ovid and Waterloo. Sponsored Links History Seneca County was formed in 1804. Seneca County is the only county in New York to officially have two county seats. The name is from the Iroquois (Seneca) that occupied part of the region. |