Background and Objective: Water Safety Plan (WSP), introduced by the WHO in 2004, represents an integrated approach and a control system based on site-specific risk analysis extended to entire water chain. It marks a fundamental step to improve the quality of water and protect human health according to the new Directive (EU) 2020/2184 on the quality of water intended for human consumption. The aim of our study was implementing a WSP in order to guarantee safety and good water quality in the internal distribution networks of the biggest University hospital in the Apulia region (Southern Italy). Methods: From January 2020 to March 2022, a microbiological monitoring programme was carried out in the water network (hot and cold water) of two hospital pavilions (A and B). Overall, a total of 3.677 water samples was analyzed for Legionella pneumophila and Pseudomonas aeruginosa detection. The results were compared with those obtained before, during and after the WSP implementation. Results: The verification monitoring revealed a progressive increasing of compliant samples for Legionella pneumophila from 76.6 up to 99.5% and from 66.4 up to 98.9% for Pavilion A and B respectively. After the water system renewal, the number of positive samples for Pseudomonas aeruginosa increased from 3.6% to 13.6% and from 3.1 to 48.7% for Pavilions A and B, respectively, with a load higher than the initial one. This contamination was totally removed by local treatments of the internal water distribution system. Conclusions: In both pavilions, the WSP brought to a reduction of Legionella pneumophila risk, thanks to the control measures adopted, removal of dead branches and constant flushing at terminal points. The presence of Pseudomonas aeruginosa was probably caused by the manipulation of water network and the detachment of the biofilm, removed subsequently by hyperchlorination and flushing treatments at the water terminal outlet points.