The aim of this study was to apply a fast and efficient protocol for monitoring levels of Legionella contamination in high-risk water systems using molecular techniques and culture methods. Forty-nine water samples from a public building were analyzed by a culture method (BCYE agar) and a specific semi-nested polymerase chain reaction (PCR). The first 30 analyses using plate counts were positive in 28% of hot water and 8% of cold water samples. The analysis by PCR, obtained within 24 h of collection, revealed the presence of DNA in 100 and 54% respectively. Only four PCR results coincided with the cultures. A second survey (19 samples) was performed 1 year later. Semi-nested PCR revealed that 53% of the samples were positive; however, plate counts yielded no positive results. The 16S rRNA sequence comparison between the first and second samplings showed 100% homology. In conclusion, the study of the design of the building's water system, the use of a fast screening semi-nested PCR and a culture method for the detection of Legionella allowed accurate assessment of the contamination, thus contributing to the early implementation of measures to eliminate the presence of the bacteria in water systems and consequently reduce a latent public health risk.