This area along the Susquehanna had long been settled by varying cultures of indigenous peoples, including those of the historic Iroquois Confederacy, who used the river for transportation, water and fishing. Around 1712 remnants of the Tuscarora tribe settled in the northern part of the town. Also an Iroquoian-speaking people, they had migrated from North Carolina, which they left because of warfare with English colonists and other tribes. In 1722, the Tuscarora were accepted by the Iroquois as the Sixth Nation of their political confederacy.
Their fortified village, Onaquaga, was an outpost of the British Colonies. A mission had been established there by the Indian Superintendent, Sir William Johnson. Mohawk and other allies of the British also became established there. Joseph Brant used it as a base for his Volunteers, which fought with the British during the American Revolutionary War. In retaliation for joint British and Iroquois raids on frontier communities, the Continental Army attacked and destroyed Onaquaga in October 1778.
It was 1785 before the region was settled again by new migrants, many of whom were Yankees from New England and veterans of the war. They formed the town of Windsor in 1807, the year following the formation of Broome County. The town was reduced in size by the creation of two other new towns in 1821: Sanford and Colesville. In 1851, a small part of Windsor was used to help form the town of Conklin. For years the economy was based on agriculture.