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Sources of drinking water have been contaminated by military-related activity for decades, but such environmental pollution has not been recognized as a security threat in its own right. The case of perchlorate in the United States demonstrates the reflexive nature of environmental security risks, as well as the inconsistent burdens of proof required for responses to uncertain threats. A known endocrine disruptor, perchlorate blocks the uptake of iodide in the thyroid, and poses a differential risk to women, children, and other at-risk groups. Despite a conclusion by the U.S. National Research Council (NRC) that known studies of perchlorate indicate no harm at low levels of ingestion (translated roughly to 27 parts per billion in water), newer research indicates a measure of concern for some tens of millions of residents in the southwestern U.S. In this article, we examine the decision-making process that translated risk assessment studies to regulatory levels, and explore how endocrine disrupting chemicals pose a methodological dilemma for chemical risk assessment policy.