The river rises in the Okefenokee Swamp, emerging at Fargo, Georgia. The river then runs southwest into Florida, dropping in elevation through limestone layers resulting in Florida's only whitewater rapids. It then turns west near White Springs, Florida, receiving the waters of the Alapaha and Withlacoochee Rivers, which together drain much of south-central Georgia. This meandering forms the southern border of Hamilton County, Florida. It then bends south near Ellaville, then southeast near Luraville, receives the Santa Fe River from the east just below Branford, then south again to the Gulf of Mexico near the town of Suwannee.
At the time of the Spanish exploration of the area in the 1530s, the river banks were inhabited by the Timucuan people, who named it Suwani, meaning "Echo River". In the 18th century, Seminoles lived by the river. The steamboat Madison operated on the river before the Civil War, and the sulphur springs at White Springs became popular as a health resort, with 14 hotels in operation in the late 1800s.
This river is the subject of the Stephen Foster song "Old Folks at Home", in which he calls it the Swanee River. Foster had named the Pedee River of South Carolina in his first lyrics. It was called Swanee River because Foster had misspelled the name Foster never saw the river he made world famous. George Gershwin's song, made popular by Al Jolson, is also spelled "Swanee", and boasts that "the folks up North will see me no more when I get to that Swanee shore".
Both these songs feature strumming banjos and reminiscences of a plantation life more typical of 19th century South Carolina along the Peedee than among the swamps and small farms of the coastal plain of Georgia and Florida. Don Ameche stars as Foster in the 1939 fictional biopic Swanee River.
When crossing the river by car today, the sign greeting visitors announces that they are crossing the Historic Suwannee River, complete with the first line of sheet music from the song. "Old Folks at Home" is the state song of Florida, designated as such in 1935. There is a Foster Museum and Carillon Tower at Stephen Foster Folk Culture Center State Park at White Springs. The spring itself is called White Sulphur Springs because of its high sulphur content. Because of a belief in the healing qualities of its waters, the Springs were long popular as a health resort.
In English parlance something going "up the Swannee" or "down the swanny" means something going badly wrong; analogous to "up the creek without a paddle".
The Lower Suwannee National Wildlife Refuge offers bird and wildlife observation, wildlife photography, fishing, canoeing, hunting, and interpretive walks. A wildlife driving tour is under construction and several boardwalks and observation towers offer views of refuge wildlife and habitat.
In recent years, the Suwannee River has been the site of music gatherings. Magnolia Festival, SpringFest, and Wannee have are held annually in Live Oak, Florida adjacent to the river. Performing artists include Vassar Clements, Peter Rowan, David Grisman, Allman Brothers Band, and the String Cheese Incident.