The Sequatchie River drains the Sequatchie Valley, a large valley in the Cumberland Plateau in eastern Tennessee.

The Sequatchie River's source is a massive spring which flows out of Devilstep Hollow Cave, a large limestone cavern. It receives the drainage of Grassy Cove, a pastoral limestone region several miles to the north from which the drainage has no surface outlet, through a spectacular series of underground passages. This cave is located in the southeastern portion of Cumberland County, and the water flowing from it is soon augmented by that of other sizeable springs and small streams, at least one of which provided enough flow for an early textile industry. The stream soon crosses into Bledsoe County and is at the floor of a valley that trends generally southwestward and is several miles wide. Natives of the area tend to call the portion of the Cumberland Plateau to the west of the valley the "Cumberland Mountains" or "the Plateau" and that to the east of it Walden Ridge or "Wallings Ridge". The Sequatchie Valley is traversed throughout much its length by U.S. Highway 127. The first sizeable town on the Sequatchie is Pikeville, county seat of Bledsoe County. State Route 30, which descends Waldens Ridge into the Valley and then climbs the escarpment back onto the Plateau, crosses here.

Crossing into Sequatchie County, the stream flows into the county seat of Dunlap. Just north of Dunlap, U.S. 127 turns southeastward, beginning the ascent onto Walden Ridge and eventually down into Chattanooga. A set of railroad tracks runs along the river from here on, testament to heavy underground coal extraction in years past. For almost the rest of its length the Sequatchie is paralleled by State Route 28. State Route 283 also runs along the base of the Waldens Ridge escarpment for several miles. The river then enters Marion County. The town of Whitwell is just a few miles into Marion County. Below Whitwell at the small community of Sequatchie (also known as Sequachee) the Sequatchie receives the flow of the Little Sequatchie River. At the Marion County seat of Jasper, which is slightly west of the river, is a railroad junction. East of town is the crossing of U.S. Highway 41 by Tennessee 28, and the bridge over the river. Shortly south of the Interstate 24 bridge is the mouth of the Sequatchie into the Guntersville Lake impoundment of the Tennessee River.