In this study, the hydrogeochemical program PHREEQC was used to determine the chemical speciation and mineral saturation indices (SIs) of groundwater in the vicinity of the proposed high-level nuclear waste repository at Yucca Mountain, Nevada (USA). In turn, these data were used to interpret the origin and recharge mode of groundwater, to elucidate the mechanisms of flow and transport, and to determine potential sources of groundwater contamination. PHREEQC was run to determine aqueous dissolved species and minerals that would be in equilibrium with the study area’s groundwater. Selected major ions, associated SI, F− and Ca/Na ion exchange were then examined using the multivariate statistical methods of principal component factor analysis and k-means cluster analysis. Analysis of dissolved ion concentrations, SIs, and Ca/Na ion exchange allows simultaneous consideration of arithmetic (raw concentrations) and logarithmic (SI, ion exchange) variables that describe the hydrochemical system and, therefore, can provide further insight into the system’s behavior. The analysis indicates that the dominant processes and reactions responsible for the hydrochemical evolution in the system are (1) evaporative concentration prior to infiltration, (2) carbonate equilibrium, (3) silicate weathering reactions, (4) limited mixing with saline water, (5) dissolution/precipitation of calcite, dolomite and fluorite, and (6) ion exchange. Principal component factor analysis and k-means cluster analysis of factor scores allow the reduction of dimensions describing the system and the identification of hydrogeochemical facies and the processes that defined and govern their evolution. Statistical analysis results indicate that the northern, west face and southern Yucca Mountain groundwater is fresh water with low concentrations of Ca2+, Mg2+, Cl−, Ca2+/(Na+)2, and CaF2. The Fortymile Wash groundwater is dilute. The carbonate signature is shown in the Ash Meadows and Death Valley waters with high fluorite SI. Finally, the Crater Flat, Stripped Hills, and Skeleton Hills are dominated by Ca/Na ion exchange, Mg and Ca. The hydrochemical and statistical analyses showed three main groundwater signatures or hydrochemical processes indicating groundwater evolution, potential flowpaths, and recharge areas. The flowpaths are the trace of the Amargosa River, the trace of Fortymile Wash, and its convergence with the Amargosa River. This appears to represent not just a groundwater flow path, but traces of surface runoff infiltration as well.