Preglacial drainage of the present Mississippi watershed was in two distinct systems. A western system headed in southern Minnesota and flowed southeastward across northeastern Iowa to Muscatine, thence southward along the present course, except for a few miles opposite the lower rapids. The eastern system from St. Paul, Minnesota, southward to the upper rapids, turned eastward at LeClaire, Iowa, and discharged through the lower part of the Illinois valley.

These drainage systems were displaced and shifted back and forth by ice sheets lying both east and west of the river. In the Nebraskan and Kansan stages disturbance by the Keewatin ice sheet initiated the cutting of a new valley from Muscatine eastward to the old eastern drainage. In the third or Illinoian stage the Labrador ice sheet covered the eastern system below Clinton, Iowa, and forced all of the drainage into a brief or temporary course through eastern Iowa outside the Illinoian ice border. When the Illinoian ice sheet melted drainage from eastern Iowa down the old valley south from Muscatine was reopened. The entire present Mississippi became established in early Wisconsin time, about 80,000 years ago. In late Wisconsin time it also carried the Glacial Lake Agassiz drainage.

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