Minnesota, lying at the northern rim of the Central Plains region, consists mainly of flat prairie, nowhere flatter than in the Red River Valley of the west. There are rolling hills and deep river valleys in the southeast; the northeast, known as Arrowhead Country, is more rugged and includes the Vermilion Range and the Mesabi Range, with its rich iron deposits. Eagle Mountain, in the extreme northeast, rises to a height of 2,301 ft (702 m), the highest point in the state; the surface of nearby Lake Superior, 600 ft (183 m) above sea level, is the state's lowest elevation.

With more than 15,000 lakes and extensive wetlands, rivers, and streams, Minnesota has more inland water than any other state except Alaska. Some of the inland lakes are quite large: Lower and Upper Red Lake, 451 sq mi (1,168 sq km); Mille Lacs, 207 sq mi (536 sq km); and Leech Lake, 176 sq mi (456 sq km). The Lake of the Woods, 1,485 sq mi (3,846 sq km), is shared with Canada, as is Rainy Lake, 345 sq mi (894 sq km). A total of 2,212 sq mi (5,729 sq km) of Lake Superior lies within Minnesota's jurisdiction.

Lake Itasca, in the northwest, is the source of the Mississippi River, which drains about three-fifths of the state and, after meeting with the St. Croix below Minneapolis–St. Paul, forms part of the eastern boundary with Wisconsin. The Minnesota River, which flows across the southern part of the state, joins the Mississippi at the Twin Cities. The Red River of the North, which forms much of the boundary with North Dakota, is part of another large drainage system; it flows north, crosses the Canadian border above St. Vincent, and eventually empties into Lake Winnipeg in Canada.

Most of Minnesota, except for small areas in the southeast, was covered by ice during the glacial ages. When the ice melted, it left behind a body of water known as Lake Agassiz, which extended into what we now call the Dakotas and Canada and was larger than the combined Great Lakes are today; additional melting to the north caused the lake to drain away, leaving flat prairie in its wake. The glaciers also left behind large stretches of pulverized limestone, enriching Minnesota's soil, and the numerous shallow depressions that have developed into its modern-day lakes and streams.