Selenium concentrations above Environmental Protection Agency safe levels are of potential concern in various parts of the Las Vegas Valley in both water and sediment media. Previous studies suggest that the source of elevated selenium in the Valley is possibly resurfacing groundwater. Shallow groundwater flows into Las Vegas Wash wetlands and therefore has important environmental implications for surface water quality and aquatic life. The objective of this study was to identify the source of selenium in the shallow groundwater of the Las Vegas Valley through a detailed geochemical analysis. A comparison of major anions and cations concentrations and the 4 trace oxyanions (Se, B, As, and Mo) in the Quaternary alluvium (Qa) zone versus Quaternary to Tertiary (QTs) zone wells show that Qa wells consistently exhibit higher concentrations of all the mentioned parameters than QTs wells. The mean Qa concentrations of the major ions and trace oxyanions ranged between 130–728% higher than the mean QTs concentrations. Study results suggest that selenium concentrations in the shallow groundwater in the Qa zone were highly correlated (p < 0.01) with the major ions: Na+ (r = 0.88), K+ (r = 0.87), SO42− (r = 0.86), NO3−-N (r = 0.74), and TDS (r = 0.84), and EC (r = 0.87) indicating a common source genesis. However, in the QTs zone, correlations among Se and the mentioned parameters were not significant. Principal component analysis performed on the major ions, EC, TDS, and Se of Qa and QTs showed that Se was one of the influencing parameters in the first principal component of Qa; however, in QTs, Se did not contribute to the variations of the first principal component. Pearson correlations further corroborated that salinity is associated with Se, B, and As in the Qa zone and only associated with B in the QTs zone. Overall, many more significant associations of Se with water quality parameters were determined in the Qa than in the older QTs formations, indicating that geological processes and formations’ mineralogy have influenced the mentioned associations.