Perchlorate (ClO4-) is a common groundwater constituent with both synthetic and natural sources. A potentially important source of ClO4- is past agricultural application of ClO4(-)-bearing natural NO3- fertilizer imported from the Atacama Desert, Chile, but evidence for this has been largely circumstantial. Here we report ClO4- stable isotope data (delta37Cl, delta18O, and delta17O), along with other supporting chemical and isotopic environmental tracer data, to document groundwater ClO4 contamination sources and history in parts of Long Island, New York. Sampled groundwaters were oxic and ClO4- apparently was not affected by biodegradation within the aquifers. Synthetic ClO4- was indicated by the isotopic method in groundwater near a fireworks disposal site at a former missile base. Atacama ClO4- was indicated in agricultural and urbanizing areas in groundwaters with apparent ages > 20 years. In an agricultural area, ClO4- concentrations and ClO4-/NO3- ratios increased with groundwater age, possibly because of decreasing application rates of Atacama NO3- fertilizers and/or decreasing ClO4- concentrations in Atacama NO3- fertilizers in recent years. Because ClO4-/NO3- ratios of Atacama NO3- fertilizers imported in the past (approximately 2 x 10(-3) mol mol(-1)) were much higher than the CO4-/NO3- ratio of recommended drinking-water limits (7 x 10(-5) mol mol(-1) in New York), ClO4- could exceed drinking-water limits even where NO3- does not, and where Atacama NO3- was only a minor source of N. Groundwater ClO4- with distinctive isotopic composition was a sensitive indicator of past Atacama NO3- fertilizer use on Long Island and may be common in other areas that received NO3- fertilizers from the late 19th century through the 20th century.