New York covers 54,475 sq miles (141,089 km²). In size, New York ranks 27th compared with the other 50 states. The Great Appalachian Valley dominates eastern New York, while Lake Champlain is the chief northern feature of the valley, which also includes the Hudson River flowing southward to the Atlantic Ocean. The rugged Adirondack Mountains, with vast tracts of wilderness, lie west of the valley. Most of the southern part of the state is on the Allegheny plateau, which rises from the southeast to the Catskill Mountains.

The western section of the state is drained by the Allegheny River and rivers of the Susquehanna and Delaware systems. The Delaware River Basin Compact, signed in 1961 by New York, New Jersey, Pennsylvania, Delaware, and the federal government, regulates the utilization of water of the Delaware system. New York's borders touch (clockwise from the north) two Great Lakes (Erie and Ontario, which are connected by the Niagara River); one former Great Lake (Lake Champlain); the provinces of Ontario and Quebec in Canada; three New England states (Vermont, Massachusetts, and Connecticut); the Atlantic Ocean, and two Mid-Atlantic states (New Jersey and Pennsylvania).

In addition, Rhode Island shares a water border with New York. While the state is best known for New York City's urban atmosphere, especially Manhattan's skyscrapers, most of the state is dominated by farms, forests, rivers, mountains, and lakes. New York's Adirondack State Park is larger than any U.S. National Park outside of Alaska. Niagara Falls, on the Niagara River as it flows from Lake Erie to Lake Ontario, is a popular attraction. The Hudson River begins with Lake Tear of the Clouds and flows south through the eastern part of the state without draining Lakes George or Champlain. Lake George empties at its north end into Lake Champlain, whose northern end extends into Canada, where it drains into the Richelieu and then the St Lawrence Rivers. Four of New York City's five boroughs are on the three islands at the mouth of the Hudson River: Manhattan Island, Staten Island, and Brooklyn and Queens on Long Island.

"Upstate" is a common term for New York State counties north of suburban Westchester, Rockland and Dutchess counties. Upstate New York typically includes the Catskill and Adirondack Mountains, the Shawangunk Ridge, the Finger Lakes and the Great Lakes in the west; and Lake Champlain, Lake George, and Oneida Lake in the northeast; and rivers such as the Delaware, Genesee, Mohawk, and Susquehanna. The highest elevation in New York is Mount Marcy in the Adirondacks.