Acidic, metal-rich waters produced by the oxidative weathering and resulting leaching of major and trace elements from pyritic rocks can adversely affect water quality in receiving streams and riparian ecosystems. Five study areas in the southern Rocky Mountains with naturally acidic waters associated with porphyry mineralization were studied to document variations in water chemistry and processes that control the chemical variations. Study areas include the Upper Animas River watershed, East Alpine Gulch, Mount Emmons, and Handcart Gulch in Colorado and the Red River in New Mexico. Although host-rock lithologies in all these areas range from Precambrian gneisses to Cretaceous sedimentary units to Tertiary volcanic complexes, the mineralization is Tertiary in age and associated with intermediate to felsic composition, porphyritic plutons. Pyrite is ubiquitous, ranging from ???1 to >5 vol.%. Springs and headwater streams have pH values as low as 2.6, SO4 up to 3700 mg/L and high dissolved metal concentrations (for example: Fe up to 400 mg/L; Cu up to 3.5 mg/L; and Zn up to 14.4 mg/L). Intensity of hydrothermal alteration and presence of sulfides are the primary controls of water chemistry of these naturally acidic waters. Subbasins underlain by intensely hydrothermally altered lithologies are poorly vegetated and quite susceptible to storm-induced surface runoff. Within the Red River study area, results from a storm runoff study documented downstream changes in river chemistry: pH decreased from 7.80 to 4.83, alkalinity decreased from 49.4 to <1 mg/L, SO4 increased from 162 to 314 mg/L, dissolved Fe increased from to 0.011 to 0.596 mg/L, and dissolved Zn increased from 0.056 to 0.607 mg/L. Compared to mine drainage in the same study areas, the chemistry of naturally acidic waters tends to overlap but not reach the extreme concentrations of metals and acidity as some mine waters. The chemistry of waters draining these mineralized but unmined areas can be used to estimate premining conditions at sites with similar geologic and hydrologic conditions. For example, the US Geological Survey was asked to estimate premining ground-water chemistry at the Questa Mo mine, and the proximal analog approach was used because a mineralized but unmined area was located adjacent to the mine property. By comparing and contrasting water chemistry from different porphyry mineralized areas, this study not only documents the range in concentrations of constituents of interest but also provides insight into the primary controls of water chemistry.