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 p CO 2 , while recharge directly into Madison outcrops has a much higher p CO 2 . 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.

Surface, unsaturated-zone, and saturated-zone hydrologic conditions at Yucca Mountain responded to past climate variations and are at least partly preserved by sediment, fossil, and mineral records. Characterizing past hydrologic conditions in surface and subsurface environments helps to constrain hydrologic responses expected under future climate conditions and improve predictions of repository performance. Furthermore, these records provide a better understanding of hydrologic processes that operate at time scales not readily measured by other means. Pleistocene climates in southern Nevada were predominantly wetter and colder than the current interglacial period. Cyclic episodes of aggradation and incision in Fortymile Wash, which drains the eastern slope of Yucca Mountain, are closely linked to Pleistocene climate cycles. Formation of pedogenic cement is favored under wetter Pleistocene climates, consistent with increased soil moisture and vegetation, higher chemical solubility, and greater evapotranspiration relative to Holocene soil conditions. The distribution and geochemistry of secondary minerals in subsurface fractures and cavities reflect unsaturated-zone hydrologic conditions and the response of the hydrogeologic system to changes in temperature and percolation flux over the last 12.8 m.y. Physical and fluid-inclusion evidence indicates that secondary calcite and opal formed in air-filled cavities from fluids percolating downward through connected fracture pathways in the unsaturated zone. Oxygen, strontium, and carbon isotope data from calcite are consistent with a descending meteoric water source but also indicate that water compositions and temperatures evolved through time. Geochronological data indicate that secondary mineral growth rates are less than 1–5 mm/m.y., and have remained approximately uniform over the last 10 m.y. or longer. These data are interpreted as evidence for hydrological stability despite large differences in surface moisture caused by climate shifts between the Miocene and Pleistocene and between Pleistocene glacial-interglacial cycles. Secondary mineral distribution and δ 18 O profiles indicate that evaporation in the shallower welded tuffs reduces infiltration fluxes. Several near-surface and subsurface processes likely are responsible for diverting or dampening infiltration and percolation, resulting in buffering of percolation fluxes to the deeper unsaturated zone. Cooler and wetter Pleistocene climates resulted in increased recharge in upland areas and higher water tables at Yucca Mountain and throughout the region. Discharge deposits in the Amargosa Desert were active during glacial periods, but only in areas where the modern water table is within 7–30 m of the surface. Published groundwater models simulate water-table rises beneath Yucca Mountain of as much as 150 m during glacial climates. However, most evidence from Fortymile Canyon up gradient from Yucca Mountain limits water-table rises to 30 m or less, which is consistent with evidence from discharge sites in the Amargosa Desert. The isotopic compositions of uranium in tuffs spanning the water table in two Yucca Mountain boreholes indicate that Pleistocene water-table rises likely were restricted to 25–50 m above modern positions and are in approximate agreement with water-table rises estimated from zeolitic-to-vitric transitions in the Yucca Mountain tuffs (less than 60 m in the last 11.6 m.y.).

Where the lower Colorado River traverses the Basin and Range Province below the Grand Canyon, significant late Pleistocene aggradation and subsequent degradation of the river are indicated by luminescence, paleomagnetic, and U-series data and stratigraphy. Aggradational, finely bedded reddish mud, clay, and silt are underlain and overlain by cross-bedded to plane-bedded fine sand and silt. That sequence is commonly disconformably overlain by up to 15 m of coarse sand, rounded exotic gravel, and angular, locally derived gravel. Luminescence dates on the fine sediments range from ca. 40 ka to 70 ka, considering collective uncertainties. A section of fine-grained sediments over a vertical range of 15 m shows normal polarity magnetization and little apparent secular variation beyond dispersion that can be explained by compaction. Aggradation on large local tributaries such as Las Vegas Wash appears to have been coeval with that of the Colorado River. The upper limits of erosional remnants of the sequence define a steeper grade above the historical river, and these late Pleistocene deposits are greater than 100 m above the modern river north of 35°N. Terrace gravels inset below the upper limit of the aggradational sequence yield 230 Th dates that range from ca. 32 ka to 60 ka and indicate that degradation of the river system in this area closely followed aggradation. The thick sequence of rhythmically bedded mud and silt possibly indicates settings that were ponded laterally between valley slopes and levees of the aggrading river. Potential driving mechanisms for such aggradation and degradation include sediment-yield response to climate change, drought, fire, vegetation-ecosystem dynamics, glaciation, paleofloods, groundwater discharge, and building and destruction of natural dams produced by volcanism and landslides.