The Iroquois River basin lies within the Interior Plains, in the Eastern Lake section of the Central Lowland province. Geomorphologists have further subdivided and classified the Iroquois Watershed as part of the Iroquois Subbasin which lies within the Upper Illinois Basin of the Upper Illinois Subregion of the Upper Mississippi Region.
The Iroquois Watershed is comprised of two major physiographic areas, the Iroquois Till Plain of the Central Till Plain Region and the Northern Moraine and Lake Plain of the Kankakee Drainageways Region. The later is often referred to as the Iroquois Moraine or Marseilles Moraine and Iroquois Lacustrine Plain. These features tend to lie in a southwest to northeast direction.