The more powerful Seneca eliminated these competing groups during the Beaver Wars beginning in 1638, as the Iroquois Confederacy sought to control the lucrative fur trade with the French and Dutch colonists.

The reservation borders both banks of the Allegheny River and is partially within several of the Towns in the south part of the county (South Valley, Cold Spring, Salamanca, Great Valley, Red House and Carrollton, with a very small portion in the town of Allegany).

The government rotates every two years, alternating operations in Jimerson Town and Irving on the Cattaraugus Reservation.

In addition to Jimerson Town, significant developed communities on the reservation include: Highbanks, a community south of Steamburg that includes residences, smoke shops, a Faithkeepers School and a campground; Shongo, a sparsely populated hamlet south of Jimerson Town; Kill Buck, a mixed community of both native and non-native residents; The Junction, a mostly commercial cluster surrounding an exit on Interstate 86; and Vandalia, the easternmost developed site on the reservation.

During the 1930s and the Great Depression, the federal government authorized a major flood control project on the Allegheny River.

The project envisioned construction of a dam and reservoir, to flood much of the Cornplanter Tract and the western portion of the Allegany Reservation.

The Seneca were compensated primarily by grants of land set aside at Jimerson Town, where numerous houses were constructed, and a handful of other resettlement areas in New York.

As of the census[4] of 2000, there were 1,099 people, 410 households, and 280 families residing in the Indian reservation (excluding the rented cities).