Cave development in the Madison aquifer of the Black Hills has taken place in several stages. Mississippian carbonates first underwent eogenetic (early diagenetic) reactions with interbedded sulfates to form breccias and solution voids. Later subaerial exposure allowed oxygenated meteoric water to replace sulfates with calcite and to form karst and small caves. All were later buried by ~2 km of Pennsylvanian–Cretaceous strata.

Groundwater flow and speleogenesis in the Madison aquifer were renewed by erosional exposure during Laramide uplift. Post-Laramide speleogenesis enlarged paleokarst voids. Most interpretations of this process in the Black Hills invoke rising thermal water, but they fail to account for the cave patterns. Few passages extend downdip below the present water table or updip to outcrops. None reaches the base of the Madison Limestone, and few reach the top. Major caves underlie a thin cover of basal Pennsylvanian–Permian Minnelusa Formation (interbedded quartzarenite and carbonates). Water infiltrating through the Minnelusa Formation dissolves carbonates in a nearly closed system, producing low pCO₂, while recharge directly into Madison outcrops has a much higher pCO₂. Both are at or near calcite saturation when they enter caves, but their mixture is undersaturated.

The caves reveal four phases of calcite deposition: eogenetic ferroan calcite (Mississippian replacement of sulfates); white scalenohedra in paleovoids deposited during deep post-Mississippian burial; palisade crusts formed during blockage of springs by Oligocene–Miocene continental sediments; and laminated crusts from late Pleistocene water-table fluctuations. The caves reveal more than 300 m.y. of geologic history and a close relationship to regional geologic events.