Naegleria fowleri is the causative agent of primary amebic meningoencephalitis (PAM), a disease of the central nervous system. Healthy humans sporadically become infected with N. fowleri and develop fatal PAM after recreational or work exposure to freshwater; accordingly, there is a need for monitoring the presence of pathogenic ameboflagellates in public freshwater. The present study was conducted to determine whether a nested PCR assay could be used for the detection of N. fowleri in freshwater habitats. Water samples were collected in Virginia, since Naegleria has been isolated previously in this state. Additionally, the occurrence of N. fowleri in samples from Connecticut was investigated since neither N. fowleri nor PAM has been reported from this region. PCR analysis demonstrated that two of four samples from Virginia were positive for N. fowleri without intervening culture while 15 of 86 samples from Connecticut were positive that had been enriched by culture. This constitutes the first report of N. fowleri from Connecticut waters. These results indicate that the PCR assay can be utilized to detect N. fowleri in water and soil collected from the environment.