After various cultures of indigenous peoples succeeded each other in the Great Lakes area, in late prehistoric times, the five nations of the Iroquois coalesced.

The current location of the Tonawanda Reservation is believed to be close to the likely poorly-defined border between the historic Seneca homeland and its rivals, the Neutral Nation that occupied the Niagara Region at the time of French missionary Joseph de La Roche Daillon's arrival in the area in 1627.

During the American Revolutionary War, most of the Iroquois sided with the British Crown, as they hoped to end colonial encroachment; to this effect, the Iroquois led several massacres on colonial settlements, which provoked the Continental Army to respond with the scorched-earth Sullivan Expedition, wiping out much of the Senecas' already destitute homelands.

After the Crown's defeat, some of the Seneca, along with other Iroquois, migrated with Joseph Brant to the Grand River reservation in the still British-controlled territory of upper Canada (now known as the province of Ontario).

Those majority of the Seneca People remained in what is now western New York, subsequently were forced to ceding lands through the Canandaigua Treaty of 1794 and the Treaty of Big Tree in 1797 which led to the reservations in western New York, which are only a fraction of their original reservation .

The Seneca of this reservation worked with self-taught anthropologist Lewis H. Morgan in mid century to teach him about the Iroquois kinship and social structures.

His insights about the significance and details of kinship structure in Native American societies influenced much following anthropological and ethnological research.

Much of the information was provided by his colleague and friend Ely S. Parker, a Seneca born on the reservation in 1828.

Over the years, the size of the reservation had been reduced by forced sales of land by the state of New York to surrounding communities.

The reservation is also noticeably more racially integrated than most Seneca Nation of Indians territories (excluding Salamanca, which operates on a lease system); whereas the Seneca Nation has actively resisted non-native settlement of its territories because of the past policy whereby white settlement meant that the tribe lost that parcel of land to Non Natives without their permission who often used it for farming.

The Census Bureau reports the part of the reservation in Genesee County has a total area of 9.3 mi2 (24.0 km2).

The northern boundary of the reservation's Niagara County portion is part of the Tonawanda Wildlife Management Area.

The United States Census Bureau compiles separate demographic data for each county's portion of the reservation.

Residents living on the Tonawanda Reservation are included in the Akron Central School District.