The Prairie du Chien Group should be viewed as two separate rock formations: the Shakopee Formation and the Oneota Dolomite. They consist mostly of carbonate rock. Fine and coarse clastic interbeds are common in the lowest part of the Oneota Dolomite.
Although small samples of these rocks have few pores and a very low to low vertical permeability, fractures and secondary pores are widely developed in parts of the units. This secondary permeability is particularly high where the Prairie du Chien Group (generally the Shakopee) is close to the ground surface. Many caves have developed within the near-surface Prairie du Chien Group. Where deeply buried, the Prairie du Chien has lower permeability and rates of water flow.
Hydrologically, the Shakopee Formation and the top part of the Oneota Dolomite form an aquifer; the lower Oneota Dolomite, which has few fractures, acts as a confining unit above the Jordan Sandstone. In the Shakopee aquifer (Shakopee and upper Oneota formations) water flows rapidly both horizontally and vertically through enlarged fractures and dissolution cavities with water flow velocities as high as 800 feet per day. In the Oneota confining unit, even though there are a few horizontal beds with dissolution features and high potential flow velocities, vertical flow is very slow. As a result, the Oneota confining unit greatly reduces the hydrologic connection between the Shakopee aquifer and the underlying Jordan Sandstone.
In the classic view, the Jordan sandstone was considered to have only flow between the grains. Recent studies, however, have shown the increasing importance of localized fractures in determining hydraulic attributes, particularly where the rock unit is close to the ground surface: Shallow Bedrock Conditions: Fracture flow rules, locally.
In Deep bedrock conditions, though, it’s still a clast thing. The lower part of the Jordan sandstone has a relatively fine grained unit which acts as a leaking confining bed between the coarser, more permeable parts of the aquifer. Permeabilities in the fine-grained unit are orders of magnitude lower than in the coarse-grained unit.
Source: Runkel, Anthony C., et al., 2003, "Hydrogeology of the Paleozoic bedrock in southeastern Minnesota:" Minnesota Geological Survey Report of Investigations 61, 105 p.