The Marmaton Watershed lies in the southeast corner of Kansas and is part of the Marais des Cynes River Basin. The Marais des Cygnes River Basin covers 4,304 square miles in east central and southeast Kansas and extends into Missouri.  Watersheds within the the Marais des Cygnes Basin include: the Upper Marais des Cygnes, Lower Marais des Cygnes, Little Osage, and the Marmaton.

For the purposes of WRAPS, the Marmaton Watershed ends at the Kansas/Missouri state line.

The water that begins in the Marmaton River travels northeast until it reaches St. Louis and the Mississippi River; therefore, it eventually ends up in the Gulf of Mexico. The map below shows the path of the water to St. Louis.