The study of Legionella in treated wastewater acquires special importance when this water is used in irrigation by spray, as Legionella is transmitted via the inhalation of aerosols and may consequently represent a health risk. In this study, we applied polymerase chain reaction (PCR) amplification as an alternative method to plate culture for detecting L. pneumophila in twelve heavily biocontaminated samples from a wastewater treatment plant. Moreover, we studied the efficiency of rapid gel filtration methods and filtration through chelating ion exchange resin in the elimination of PCR inhibitors from wastewater samples. When Legionella was investigated by PCR without any previous treatment, no amplification occurred, and when we used chromatographic methods to eliminate PCR inhibitors, nine out of twelve samples became positive. These results indicate the abundant presence of Legionella in wastewater, and although the methods used to eliminate PCR inhibitors are effective in the preparation of clean samples, the possible presence of different metal-organic matter compounds, which are not eliminated, may produce false-negative results.