Mixed carbonate-siliciclastic sediments of the Prairie du Chien Group were largely deposited in shallow tropical seas. Sedimentologic indices of shallow-water deposition and a moderately diverse Early Ordovician macrofauna and mid-continent conodont fauna indicate that shallow-marine conditions prevailed across the Wisconsin arch and Michigan basin throughout most of Prairie du Chien deposition. Although the Wisconsin arch and Michigan basin were weakly active structural features, tectonism does not appear to have appreciably influenced water depths. The Michigan basin was not a bathymetric basin during the Early Ordovician as it became during the Silurian.

The Prairie du Chien Group contains two major depositional sequences, the Oneota and Shakopee formations, both of which are bounded by type 1 sequence boundaries. On the Wisconsin arch, type 1 sequence boundaries are associated with karsting and silicification of underlying carbonates, indicating unconformity development during prolonged subaerial exposure. In the central Michigan basin, formation contacts are sharp and appear disconformable. The contacts between the two lithostratigraphic members comprising each formation in outcrop do not appear to be subaerial unconformities and are interpreted as type 2 sequence boundaries.

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