Geochemical study of water and gas discharging from the deeply incised aquifer system at the Grand Canyon, Arizona, provides a paradigm for understanding complex groundwater mixing phenomena, and Quaternary travertines deposited from cool springs provide a paleohydrologic record of this mixing. Geochemical data show that springs have marked compositional variability: those associated with active travertine accumulations (deeply derived endogenic waters) are more saline, richer in CO2, and elevated in 87Sr/86Sr relative to springs derived dominantly from surface recharge of plateau aquifers (epigenic waters). Endogenic waters and associated travertine are preferentially located along basement-penetrating faults. We propose a model whereby deeply derived fluids are conveyed upward via both magmatism and seismicity. Our model is supported by: (1) gas analyses from spring waters with high He/Ar and He/N2 and 3He/4He ratios indicating the presence of mantle-derived He; (2) large volumes of travertine and CO2-rich gases in springs recording high CO2 fluxes; and (3) 87Sr/86Sr in these springs that indicate circulation of waters through Precambrian basement. Geochemical trends are explained by mixing of epigenic waters of the Colorado Plateau aquifers with different endogenic end-member waters in different tectonic subprovinces. Endogenic waters are volumetrically minor but have significant effects on water chemistry. They are an important and largely unrecognized component of the hydrogeochemistry and neotectonics of the southwestern United States.