Perchlorate (ClO4-) in groundwater can be from synthetic or natural sources, the latter of which include both historical application of imported nitrate fertilizers from the Atacama Desert of Chile and naturally deposited ClO4- that forms atmospherically and accumulates in arid regions such as the southwestern US. The objective of this study was to evaluate the use of isotopic data to distinguish sources of ClO4- in groundwater in a specific region of the Rialto-Colton and Chino, CA groundwater subbasins (Study Area). This region includes two groundwater ClO4- plumes emanating from known military/industrial source areas, and a larger area outside of these plumes having measurable ClO4-. Perchlorate extracted from wells in this region 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. Isotope data indicate synthetic, Atacama, and indigenous natural ClO4- were present in the Study Area. Stable isotope data from nearly all sampled wells within the contours of the two characterized plumes, including those located in a perched zone and within the regional groundwater aquifer, were consistent with a dominant synthetic ClO4- source. In wells downgradient from the synthetic plumes and in the Chino subbasin to the southwest, isotopic data indicate the dominant source of ClO4- largely was Atacama, presumably from historical application of nitrate fertilizer in this region. Past agricultural land use and historical records are consistent with this source being present in groundwater. The 36Cl and δ18O data indicate that wells having predominantly synthetic or Atacama ClO4- also commonly contained small fractions of indigenous natural ClO4-. The indigenous ClO4- was most evident isotopically in wells having the lowest overall ClO4- concentrations (< 1 μg/L), consistent with its occurrence as a low-level background constituent in the region. A small subset of wells outside the contours of the two synthetic plumes, including an upgradient well, had characteristics indicating small amounts of synthetic ClO4- mixed with one or both of the natural source types. Hydrogeologic data indicate synthetic ClO4- in the upgradient well may be from a source other than the identified plume sources, but it is not known whether this source might also be present in other wells at low concentrations. The stable isotope and 36Cl data provided relatively unambiguous discrimination of synthetic and Atacama ClO4- sources in most wells having relatively high concentrations, providing regional perspective on anthropogenic ClO4- contamination in the Rialto-Colton and Chino subbasins. Where indigenous natural ClO4- was indicated as a substantial component, total ClO4- concentrations were low and concentrations of anthropogenic components were near background levels.