Concentrations of twenty-seven elements, including naturally-occurring water-quality contaminants arsenic, chromium, and uranium, were measured in 217 samples of alluvium and rock from the western Mojave Desert, southern California, using portable (pXRF) and laboratory (LXRF) X-ray fluorescence. Comparison of measurements with NIST-traceable standards was good, although pXRF overestimated iron compared to LXRF. Results suggest pXRF survey data are sufficiently accurate to assess regional geochemical differences in geologic-source terrains. Principal component analysis showed rubidium and potassium were associated with alluvium eroded from felsic terrain, while iron, copper, chromium, and to a lesser extent titanium, manganese, and nickel were associated with alluvium eroded from mafic terrain. Zinc, vanadium, and arsenic were associated with alluvium eroded from hydrothermal terrain. Elemental assemblages associated with different source terrains were traced spatially to identify the source and composition of alluvium composing aquifers pumped for water supply. Changes in geologic source terrain to the Mojave River, associated with movement along the San Andreas Fault over the past one to five million years, reduced the mafic fraction and increased the felsic fraction of alluvium deposited to the regionally important floodplain aquifer along the Mojave River—lowering chromium concentrations in alluvium through geologic time. Comparison of pXRF and sequential extraction data from 40 samples showed arsenic and uranium were more abundant on the surfaces of mineral grains, while chromium and vanadium remained mostly within unweathered mineral grains—suggesting arsenic and uranium may be more readily mobilized into groundwater with changes in pH, redox, or ionic strength than chromium or vanadium.