The Des Moines River drains about 1,350 square miles (3,496 km2) of the north, west, and central parts of the watershed, and the East Fork Des Moines River along with several small creeks drain about 200 square miles (518 km2) in the east part. These tributaries join the Des Moines river in Iowa.
The watershed is on the Coteau des Prairies, the most prominent upland in southern Minnesota. the Coteau rises to altitudes of more than 1,900 feet (579 m) within the watershed. The west boundary is along the crest of the Coteau and was formed by a terminal moraine during late Wisconsin Glaciation. This moraine forms part of the divide between the Mississippi and Missouri Rivers. The north and east boundaries are also formed by morainic highs which represent recessions of the Des Moines lobe during late Wisconsin Glaciation. Surficial materials consist mostly of clayey drift with a few surficial outwash (sand and gravel) areas near the streams.
Topographic quadrangle maps published by the U.S. Geological Survey are available for the entire watershed.