Naegleria fowleri causes the usually fatal disease primary amebic meningoencephalitis (PAM), typically in people who have been swimming in warm, untreated freshwater. Recently, some cases in the United States were associated with exposure to treated drinking water. In 2013, a case of PAM was reported for the first time in association with the exposure to water from a U.S. treated drinking water system colonized with culturable N. fowleri. This system and another were found to have multiple areas with undetectable disinfectant residual levels. In response, the water distribution systems were temporarily converted from chloramine disinfection to chlorine to inactivate N. fowleri and reduce biofilm in the distribution systems. Once >1.0 mg/L free chlorine residual was attained in all systems for 60 days, water testing was performed; N. fowleri was not detected in water samples after the chlorine conversion. This investigation highlights the importance of maintaining adequate residual disinfectant levels in drinking water distribution systems. Water distribution system managers should be knowledgeable about the ecology of their systems, understand potential water quality changes when water temperatures increase, and work to eliminate areas in which biofilm growth may be problematic and affect water quality.