The county is bisected by the Genesee River, flowing north to its mouth on Lake Ontario.

During the mid-nineteenth century, the Genesee Valley Canal was built to link southern markets to the Great Lakes and Mohawk River.

Part of the Oil Springs Reservation, controlled by the Seneca Nation, is located in the county.

European-American permanent settlement did not take place until after the American Revolutionary War and the forced cession by the Seneca of most of their lands in western New York.

New York State sold off the lands cheaply to attract new European-American settlers and agricultural development.

The first County Seat was established at Angelica, New York, where it remained for half a century.

[7] However, on April 13, 1814, the eastern half of Cattaraugus County was so attached and administered from Belmont.

[13] Allegany County is in the southwestern part of New York State, along the Pennsylvania border.

The highest point in the county is Alma Hill, with an elevation of 2,548 feet (777 meters) above sea level.

The highest point of Interstate 86 is located in the town of West Almond with an elevation of 2,110 feet.

The county is unique from a watershed perspective as it is providing water to three major watersheds of North America: The eastern part near Alfred has Canacadea Creek that goes into the Canisteo River, Susquehanna River and eventually to Chesapeake Bay.

The Genesee River bisects the county from south to north, flowing north out of the County through Letchworth State Park with its three waterfalls on to Rochester over three more waterfalls to its mouth on Lake Ontario and then on to the St. Lawrence River and Atlantic Ocean.

In June 1972 the remnants of Hurricane Agnes stalled over the area, dropping more than 20 inches (510 mm) of rain.

Long a necessary transportation waterway for the Seneca and other Native Americans, and successive European-American settlers, since the late 20th century, the Genesee River has been extremely popular with canoeists.

[22] It has been reported that in the last 170 years, the only Democratic candidates to win were Franklin Pierce in 1852[23] and Lyndon B. Johnson in 1964.

[24] Even in 1964, when Republican nominee Barry Goldwater lost the county by 14 points, he still managed to carry the towns of Centerville, Caneadea, Granger, Hume, and Rushford.

[25] In 2006, neither Democrat Eliot Spitzer nor Hillary Clinton carried it in their otherwise landslide elections for governor and US senator, respectively.

This is the site of the famed spring described by the Franciscan Missionary Joseph DeLa Roch D'Allion in 1627, the first recorded mention of oil on the North American Continent.

The remainder of the reservation is mostly utilized for cottages on Cuba Lake, Seneca-run gas stations, and woodlands.