The processes that affect water chemistry as the water flows from recharge areas through breccia-pipe uranium deposits in the Grand Canyon region of the southwestern United States are not well understood. Pigeon Spring had elevated uranium in 1982 (44 μg/L), compared to other perched springs (2.7–18 μg/L), prior to mining operations at the nearby Pigeon Mine. Perched groundwater springs in an area around the Pigeon Mine were sampled between 2009 and 2015 and compared with material from the Pigeon Mine to better understand the geochemistry and hydrology of the area. Two general groups of perched groundwater springs were identified from this study; one group is characterized by calcium sulfate type water, low uranium activity ratio ²³⁴U/²³⁸U (UAR) values, and a mixture of water with some component of modern water, and the other group by calcium-magnesium sulfate type water, higher UAR values, and radiocarbon ages indicating recharge on the order of several thousand years ago. Multivariate statistical principal components analysis of Pigeon Mine and spring samples indicate Cu, Pb, As, Mn, and Cd concentrations distinguished mining-related leachates from perched groundwater springs. The groundwater potentiometric surface indicates that perched groundwater at Pigeon Mine would likely flow toward the northwest away from Pigeon Spring. The geochemical analysis of the water, sediment and rock samples collected from the Snake Gulch area indicate that the elevated uranium at Pigeon Spring is likely related to a natural source of uranium upgradient from the spring and not likely related to the Pigeon Mine.