The military has been using manufactured perchlorate since the early 1900s. It is best known for military uses, Mayer said, because so many contaminated sites, especially in California, are linked to defense operations. In other cases, though, there is no clear source for the presence of perchlorate.
To distinguish natural from man-made perchlorate, scientists began using isotopic signatures. They discovered perchlorate atoms that formed naturally have a different number of neutrons than manufactured ones, so the atomic masses differ. The technology is still largely used in research, Jackson said.
Key questions facing EPA and others are where perchlorate is located and how toxic it is, Mayer said. Over the past decade, scientists have been working on those questions, and they still have not found satisfactory answers.
Perchlorate is a salt that accumulates underground just below the soil surface.
In wetter areas, the salts get flushed out, but they accumulate in deserts. The Atacama Desert in Chile has some of the highest levels of the chemical, and Chilean fertilizer, which is exported, has had historically high perchlorate concentrations.
Perchlorate remained in desert areas like the Atacama and throughout the southwest United States until farmers began tilling the soil. As it got stirred around, perchlorate entered groundwater in some areas, Texas Tech's Jackson said.
But how the perchlorate got there continues to puzzle researchers, who have not learned exactly what causes perchlorate to form, Jackson said. It is probably produced in the atmosphere and deposited on the ground, he said, but this process is not well understood.
Scientists are now examining mechanisms that could be causing perchlorate formation. Jackson said atmospheric ozone is certainly involved in some cases, while lightning could also play a role. Another possible explanation is surface oxidation, by which chlorine on the soil's surface might react with oxygen to form perchlorate.
"There are probably various mechanisms -- all high-energy -- but we don't have a good handle on that," USGS's Stonestrom said. "It's still an area of active research."
Perchlorate's effects on human health are no mystery.
It has been known since the 1950s that high doses of perchlorate can disrupt thyroid function and hormone production. Perchlorate was used then to treat overactive thyroids, which cause neurological and behavioral problems in children.
But the questions that remain about what levels of exposure cause problems vex health experts and regulators.
A 2006 study by the Centers for Disease Control and Prevention found a statistical association between low amounts of perchlorate and observed changes in thyroid function in women with low iodine levels. The thyroid gland absorbs iodide from the blood to make and release hormones. The study did not establish a cause-and-effect relationship but pointed to a need for more research, said Benjamin Blount, the lead author and head of CDC's perchlorate biomonitoring lab.
"We need to do studies to explore the perchlorate exposure levels in the general population, especially in more sensitive subgroups," including pregnant and nursing women and infants, Blount said.
Expressing surprise at the results of the CDC study, Thomas Zoeller, a perchlorate expert at the University of Massachusetts, asked, "The question is, does a high-dose, short-term experiment predict a long-term, low-dose effect?"
The questions for EPA are whether those people could be hurt by perchlorate in drinking water and at what concentrations damage begins. EPA has set an interim health advisory level of 15 ppb for drinking water, the highest level that the most sensitive populations -- pregnant women, in this case -- should ingest.