The study aimed to assess the prevalence of Legionella spp. in dental unit waterlines of a dental clinic and to verify whether the microbiological parameters used as indicators of water quality were correlated with Legionella contamination. A risk management plan was subsequently implemented in the dental health care setting, in order to verify whether the adopted disinfection protocols were effective in preventing Legionella colonization. The water delivered from syringes and turbines of 63 dental units operating in a dental clinic, was monitored for counts of the heterotrophic bacteria P. aeruginosa and Legionella spp. (22 °C and 37 °C). At baseline, output water from dental units continuously treated with disinfection products was more compliant with the recommended standards than untreated and periodically treated water. However, continuous disinfection was still not able to prevent contamination by Legionella and P. aeruginosa. Legionella was isolated from 36.4%, 24.3% and 53.3% of samples from untreated, periodically and continuously treated waterlines, respectively. The standard microbiological parameters used as indicators of water quality proved to be unreliable as predictors of the presence of Legionella, whose source was identified as the tap water used to supply the dental units. The adoption of control measures, including the use of deionized water in supplying the dental unit waterlines and the application of a combined protocol of continuous and periodic disinfection, with different active products for the different devices, resulted in good control of Legionella contamination. The efficacy of the measures adopted was mainly linked to the strict adherence to the planned protocols, which placed particular stress on staff training and ongoing environmental monitoring.