Perchlorate (ClO₄⁻) in groundwater can be from synthetic or natural sources. Natural sources include ClO₄⁻ associated with historical application of imported natural nitrate fertilizer from the Atacama Desert of Chile, and indigenous ClO₄⁻ that accumulates locally in arid regions from atmospheric deposition. The Rialto-Colton groundwater subbasin, 80 km east of Los Angeles, California, includes two mapped ClO₄⁻ plumes from known military/industrial sources. Larger areas downgradient from those plumes, and in the Chino subbasin to the southwest, also contain ClO₄⁻. Perchlorate from wells was analyzed for chlorine and oxygen stable isotope ratios (δ³⁷Cl, δ¹⁸O, Δ¹⁷O) and radioactive chlorine-36(³⁶Cl) isotopic abundance, along with other geochemical, isotopic, and hydrogeologic data. Isotopic data show that synthetic ClO₄⁻ was the dominant source within the mapped plumes. Downgradient from the mapped plumes, and in the Chino subbasin, the dominant source of ClO₄⁻ was related to past agricultural use of Chilean (Atacama) nitrate fertilizer. The ³⁶Cl and δ¹⁸O data indicate that wells having predominantly synthetic or Atacama ClO₄⁻ also contained small fractions of indigenous ClO₄⁻. Little or no differences were observed in isotopic composition or ClO₄⁻ source with depth in depth-dependent data from selected wells. Indigenous ClO₄⁻ was most evident in upgradient wells having ClO₄⁻ concentrations <1 μg/L, consistent with its occurrence as a background constituent throughout the region. Stable isotope ratios of chlorine and oxygen and ³⁶Cl isotopic abundance data provided relatively unambiguous discrimination of synthetic and Atacama sources in most wells having ClO₄⁻ concentrations greater than 1 μg/L.