Perchlorate (ClO₄⁻) has been detected widely in groundwater and soils of the southwestern United States. Much of this ClO₄⁻ appears to be natural, and it may have accumulated largely through wet and dry atmospheric deposition. This study evaluates the isotopic composition of natural ClO₄⁻ indigenous to the southwestern U.S. Stable isotope ratios were measured in ClO₄⁻ (δ¹⁸O, Δ¹⁷O, δ³⁷Cl) and associated NO₃⁻ (δ¹⁸O, Δ¹⁷O, δ¹⁵N) in groundwater from the southern High Plains (SHP) of Texas and New Mexico and the Middle Rio Grande Basin (MRGB) in New Mexico, from unsaturated subsoil in the SHP, and from NO₃⁻-rich surface caliche deposits near Death Valley, California. The data indicate natural ClO₄⁻ in the southwestern U.S. has a wide range of isotopic compositions that are distinct from those reported previously for natural ClO₄⁻ from the Atacama Desert of Chile as well as all known synthetic ClO₄⁻. ClO₄⁻ in Death Valley caliche has a range of high Δ¹⁷O values (+8.6 to +18.4 ‰), overlapping and extending the Atacama range, indicating at least partial atmospheric formation via reaction with ozone (O₃). However, the Death Valley δ³⁷Cl values (−3.1 to −0.8 ‰) and δ¹⁸O values (+2.9 to +26.1‰) are higher than those of Atacama ClO₄⁻. In contrast, ClO₄⁻ from western Texas and New Mexico has much lower Δ¹⁷O (+0.3 to +1.3‰), with relatively high δ³⁷Cl (+3.4 to +5.1 ‰) and δ¹⁸O (+0.5 to +4.8 ‰), indicating either that this material was not primarily generated with O₃ as a reactant or that the ClO₄⁻ was affected by postdepositional O isotope exchange. High Δ¹⁷O values in ClO₄⁻ (Atacama and Death Valley) are associated with high Δ¹⁷O values in NO₃⁻, indicating that both compounds preserve characteristics of O₃-related atmospheric production in hyper-arid settings, whereas both compounds have low Δ¹⁷O values in less arid settings. Although Δ¹⁷O variations in terrestrial NO₃⁻ can be attributed to mixing of atmospheric (high Δ¹⁷O) and biogenic (low Δ¹⁷O) NO₃⁻, variations in Δ¹⁷O of terrestrial ClO₄⁻ are not readily explained in the same way. This study provides important new constraints for identifying natural sources of ClO₄⁻ in different environments by multicomponent isotopic characteristics, while presenting the possibilities of divergent ClO₄⁻ formation mechanisms and(or) ClO₄⁻ isotopic exchange in biologically active environments.