Increasingly, regulatory agencies are adopting restrictive rules limiting the concentration of nitrogen in effluent discharged to land from decentralized wastewater treatment systems. These effluent limits are often modeled after the federal drinking water standard (Maximum Contaminant Level, or MCL) for nitrate, set at 10 mg/L nitrate-N. By law, the MCL applies only to public drinking water supplies, and not to wastewater treatment system discharges. Nevertheless, restrictive effluent limits derived from the MCL are often imposed by regulatory agencies that believe such measures are necessary to protect groundwater resources and to protect the public from health risks attributed to nitrate. The supposed risks include methemoglobinemia (“blue-baby syndrome”), increased incidence of cancer, and adverse reproductive effects. In this paper, we discuss published epidemiological and medical research on this subject spanning over five decades, and make the case that convincing, reproducible scientific evidence to substantiate health-risk claims has failed to materialize. Health authorities often take for granted that drinking water nitrate may cause blue-baby syndrome when nitrate is converted into nitrite by bacteria in the infant's upper digestive tract. That outdated theory is inconsistent with numerous observations suggesting that another factor must be responsible. We discuss compelling evidence consistent with the emerging theory, which holds that the underlying cause of drinking water associated blue-baby syndrome is gastrointestinal disturbance resulting from unsanitary wells contaminated with fecal microorganisms. We also discuss the findings of studies that examined the relationship between nitrate and incidence of cancer and reproductive effects. Considering that definitive evidence of nitrate health risks is conspicuously lacking, we call for a more rational approach to setting effluent limits for waste treatment systems, one that considers costs/benefits and recognizes factors such as nitrogen removal in the soil, aquifer characteristics, and dilution, all of which can attenuate nitrogen in the soil and receiving groundwater.