Ballston Spa is a village in Saratoga County, New York, United States. The population was 5,556 at the 2000 census. It is the county seat of Saratoga County. The village is named after Rev. Eliphalet Ball, a Congregationalist clergyman and an early settler. The village lies on the border of two towns and is partly in the Town of Ballston and partly in the Town of Milton. The village is southwest of Saratoga Springs.