Jewel Cave National Monument and Wind Cave National Park in South Dakota contain two of the six longest caves worldwide. These caves contain subterranean lakes that are important points of intersection between the water table of the Madison aquifer and the caves. During 2015 to 2017, several subterranean lakes were discovered in Jewel Cave, which previously was thought to be above the regional water table. The objectives of this study were to better understand the hydrology of the recently discovered lakes in Jewel Cave and to evaluate their relation or possible connection to similar subterranean lakes in Wind Cave. Both objectives align with National Park Service resource management purposes. Multivariate analysis, consisting of principal component analysis (PCA), cluster analysis, and end member mixing, was applied to hydrochemical data for 70 sites within and surrounding Jewel Cave and Wind Cave. Hydrochemical data consisted of the contents of major ions (Ca, Mg, Na, HCO3, Cl, Si, SO4), arsenic (As), strontium (Sr), uranium (U), stable isotopes of oxygen and hydrogen (δ18O, δ2H), radiogenic isotope ratios of strontium and uranium (87Sr/86Sr and 234U/238U), pH, and electrical conductivity (EC) in water samples. Five hydrogeologic domains were identified on the basis of PCA and cluster analysis for the area encompassing Jewel Cave and Wind Cave in the southern Black Hills. The Artesian 1 and Artesian 2 domains represent primarily artesian springs and surrounding groundwater, the East and West domains represent areas where Madison and Minnelusa aquifer rocks are at or near the land surface, and the Precambrian domain represents the Precambrian aquifer. Multivariate analysis indicates that the Jewel Cave area is part of the West domain and that Wind Cave is part of the East domain. End member mixing was applied to estimate that groundwater in the Jewel Cave area primarily was derived from the West domain and secondarily from the Precambrian domain. Jewel Cave and Wind Cave contain lakes that are well connected to regional groundwater flow in the Madison aquifer.