The Choctawhatchee River originates as two separate forks (East Fork and West Fork) in wetlands near Clayton in Barbour County. The East and West Forks flow through areas with more species of trees than any other forest in temperate North America. Near Ozark in central Dale County, the forks merge to form the Choctawhatchee River which flows southeast for about 48 miles to Geneva.

The Choctawhatchee River is one of the longest free-flowing rivers remaining in Alabama and drains an area of 3,484 square miles. Its main tributary, the Pea River, joins the Choctawhatchee just below Geneva near the Florida state line. Forests cover approximately 43% of the watershed with 26% in pasture and cropland.