The Mississippian System has the largest subcrop area of any Phanerozoic system in the Michigan Basin, and attains a maximum thickness of 719 m (2,360 ft) northeast of the basin center. The Mississippian formations include, in ascending stratigraphic order: Antrim Shale, the laterally equivalent Bedford and Ellsworth Shales (all Upper Devonian to Kinderhookian); Berea Sandstone (Kinderhookian); Sunbury Shale (Kinderhookian); Coldwater Shale (Kinderhookian to Osagian); Marshall Sandstone (Osagian); Michigan Formation (Osagian to Meramecian); and Bayport Limestone (Meramecian). There are no Chesterian sediments in the Michigan Basin. The Mississippian sediments accumulated conformably on Devonian strata but are overlain with disconformity by Pennsylvanian and, very locally, Jurassic strata.

The Kinderhookian, Osagian, and Meramecian series record a decreasing rate of Michigan Basin subsidence through time. Subsidence ceased temporarily during the Chesterian Epoch, and some Mississippian units were eroded from local anticlines in the central basin area during this interval of nondeposition. As a result, basal Pennsylvanian strata rest directly on Meramecian rocks and locally on older Mississippian formations.

The Mississippian sediments are primarily shallow-marine deposits consisting largely of shale with subordinate amounts of sandstone, siltstone, carbonates, and evaporites. Fluvial-deltaic deposits make up a significant portion of the section only in the eastern half of the basin. Terrigenous clastics were derived mainly from a source to the northeast of the basin in the Canadian Shield and, to a lesser extent, from the northwest in the Wisconsin Highlands.

Significant quantities of oil and gas have been produced from sandstones in the Berea, Marshall, and Michigan Formations, and from carbonates in the Ellsworth Shale. Sandstones in the Coldwater and Marshall Formations were, at one time, extensively quarried for grindstones and construction flagstone, respectively. The Michigan Formation is the chief source of gypsum in Michigan, and the Bayport supplies some of the state’s limestone.