The Late Devonian Michigan Basin was floored by the Middle and Upper Devonian Squaw Bay Limestone, which was deposited during the downwarping that produced the basin within a former Middle Devonian carbonate platform. The Squaw Bay comprises three beds, each having a different conodont fauna. The two upper beds, deposited during the transitans Zone, have different conodont biofacies that reflect this deepening. The basin was largely filled by the deep-water, anaerobic to dysaerobic, organic-rich, black Antrim Shale, which has a facies relationship with the prodeltaic, greenish gray Ellsworth Shale that prograded into the basin from the west. The Upper Devonian (Frasnian to Famennian) Antrim Shale is divided into four members, from base to top: the Norwood, Paxton, Lachine, and upper members. These members are more or less precisely dated by conodonts. The Norwood was deposited during the transitans Zone to Ancyrognathus triangularis Zone, and the Paxton was deposited from that zone probably through the linguiformis Zone at the end of the Frasnian. The overlying Lachine was deposited during the early Famennian and has yielded faunas of the Upper crepida and Lower rhomboidea Zones. Only the lower part of the upper member is exposed, and near Norwood, Michigan, it yielded conodonts of the Lower marginifera Zone. The widespread Famennian floating plant Protosalvinia (Foerstia) has not yet been found in outcrops of the Antrim, and should not be expected to occur except in the upper member or highest part of the Lachine Member. Its range in terms of conodont zones is from the Upper trachytera Zone through the Lower expansa Zone and possibly into the Middle expansa Zone. One known subsurface occurrence might be datable as rhomboidea or Lower marginifera Zone, depending on gamma ray correlations to outcrops. Black shale deposition ended when the Late Devonian mud delta of the Bedford Shale prograded across the Michigan Basin from the east and then retreated as the regressive Berea Sandstone was being deposited during the major eustatic sea-level fall that ended the Devonian. The Bedford was deposited during the Upper expansa to Lower praesulcata Zones, and the Berea was deposited during the Middle to Upper praesulcata Zones. Both formations contain the spore Retispora lepidophyta, which is a global indicator of latest Devonian age.

The Upper Devonian sequence in the Michigan Basin is a westward extension of coeval cyclical facies of the Catskill deltaic complex in the Appalachian basin. Both basins and the intervening Findlay arch express the tectonic and sedimentational effects of foreland compression and isostatic compensation produced by the Acadian orogeny. The Late Devonian Michigan Basin formed as one of several local deeps within the long Eastern Interior seaway that separated the North American craton, backboned by the Transcontinental arch, on the west from the Old Red continent, Avalon terrane (microplate), and possibly northwest Africa on the east. Basin development began in the late Middle Devonian (late Givetian varcus Zone) with subsidence of a shallow-water carbonate platform formed by rocks of the Traverse Group. Subsidence was contemporaneous with Taghanic onlap of the North American craton. During subsidence, a thin transitional sequence of increasingly deeper water limestones separated by hardgrounds was deposited in the incipient Michigan Basin during the latest Givetian to earliest Frasnian disparilis to falsiovalis Zones. Deposition of this sequence culminated during the early Frasnian transitans Zone with a calcareous mudstone bed at the top of the Squaw Bay Limestone. Subsidence was followed by a 12-m.y.-long Late Devonian episode of slow, hemipelagic, basinal sedimentation of organic black muds that formed the Antrim Shale, interrupted basinwide only by deposition of its prodeltaic Paxton Member. Westward, the basinal Antrim black muds intertongued with greenish gray, deltaic and prodeltaic muds of an eastward-prograding delta platform formed by the Ellsworth Shale. Basinal black shale deposition ceased in latest Devonian (late Famennian Lower praesulcata Zone) time, when the Bedford deltaic complex prograded westward, completely filling the Antrim Basin and even covering part of the older Ellsworth deltaic complex on the west. As sea level was lowered eustatically near the end of the Devonian, the regressive Berea Sandstone terminated deltaic deposition. After an Early Mississippian erosional episode, widespread deposition of the unconformably overlying Lower Mississippian Sunbury Shale began during the next transgression, associated with a major eustatic rise in the Lower crenulata Zone.

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.