Near Willacoochee, Georgia, the Alapaha collects the Willacoochee River. In Florida, it collects the Alapahoochee River and the short Little Alapaha River, which rises in Echols County, Georgia, and flows southwestward.
The Alapaha River is an intermittent river for part of its course. During periods of low volume, the river disappears underground and becomes a subterranean river. At approximately 2.3 miles (3.7 km) downstream from Jennings, Florida is a river sinkhole variously known as the Alapaha River Sink, Suck Hole, or the Devil's Den on the western bank of the river. A few more miles downstream is a second sinkhole known as the Dead River Sink or the Siphon. At the latter point during the periods of low water flow, the river disappears underground leaving a dry bank for much of the remainder of its course. The Alapaha River later reappears at the Alapaha River Rise, which is about a half mile upstream from the confluence of the Alapaha River and the Suwanee River. During a period of low rainfall over 11 miles (17.7 km) of the riverbed can be dry as the river goes underground.