The Blackwater River was named from the character of its banks and water.

[4] The Blackwater River is formed by the confluence of the North Fork Blackwater River and the South Fork Blackwater River in Johnson County approximately 6 miles (10 km) northwest of Warrensburg.

The river flows generally east-northeastwardly through Johnson, Pettis, Saline and Cooper counties, past the towns of Sweet Springs and Blackwater.

It flows into the Lamine River in northwestern Cooper County, approximately 4 miles (6.4 km) southeast of Blackwater.

The North Fork source is in the southwestern corner of Lafayette County near the small village of Chapel Hill and the South fork source is just to the southwest across the county line in the northwest corner of Johnson County.