The natural waters associated with Yucca Mountain include precipitation (rain and melted snow), ephemeral surface waters, soil waters, vadose zone pore waters, perched waters and saturated zone ground waters. Using precipitation compositions as a starting point, chemical and isotopic data for the other water types are evaluated to identify significant processes that may control their compositions. The ratios of Cl− to each of the other major constituents in precipitation waters are used to evaluate gains or losses of major ions in the other waters. Evapotranspiration of precipitation waters in the soil zone appears to be a very important process in the control of vadose zone pore waters, perched waters and saturated zone ground water compositions. In the desert climate associated with the Yucca Mountain site, this process leads to the precipitation of salts and silica in the soil zone. Surface waters sampled near the site have preferentially dissolved soil zone chlorides, sulfates, carbonates, and silica. Pore waters extracted from bedded tuffs of the upper Paint Brush Tuff in Yucca Mountain have ratios of Ca, Na, HCO3 and SO4 to Cl that are all lower than those found in precipitation. The lower ratios likely reflect precipitation of alkaline earth carbonates and possibly sulfates in the soil zone. Pore waters extracted from the Calico Hills Tuff also appear to reflect the precipitation of alkaline earth sulfates in the soil zone. Alternatively, the low SO4 to Cl ratios observed in these waters reflect variations in precipitation compositions with time. Perched waters are more dilute than vadose zone pore waters but appear to have gained their solutes by similar mechanisms. For perched waters, sulfates were dissolved in the soil zone in addition to carbonates and chlorides. The dissolution of the less soluble phases (i.e. alkaline earth carbonates and sulfates) in the soil zone implies perched waters were infiltrated under wetter climatic conditions. Saturated zone waters originated by processes similar to those that formed the perched waters except that the former were subject to more extensive ion exchange reactions. Ground waters in the shallow saturated zone beneath Yucca Mountain appear to include a significant component that was locally infiltrated. Deeper saturated zone waters likely infiltrated further upgradient in the direction of Pahute Mesa.