Biofilms in dental unit waterlines (DUWL) are a potentially significant source of contamination posing a significant health risk as these may come into contact with patients and dental staff during treatment. The aim of this study was to evaluate the microbiological quality of DUWL water treated by Biofilm-Removing-System® (BRS®) and Alpron®/Bilpron® disinfectant solutions for six years in a French university hospital. The microbiological quality of water supplied by 68 dental units—initially shock treated with BRS®, then continuously treated by Alpron® with sterile water during working days and Bilpron® during inactivity period, and combined with purging every morning and after each patient—was assessed biannually during six years for total culturable aerobic bacteria at 22 °C and 36 °C, Legionella sp., Pseudomonas aeruginosa, and total coliforms. A total of 628 samples were analyzed, 99.8% were compliant with extended microbiological levels, and we never detected pathogen bacteria like Legionella sp. and P. aeruginosa. Only one sample (0.2%) was noncompliant with the level of total culturable aerobic bacteria at 36 °C, which exceeded 140 colony forming units per mL. The protocol implemented in our university hospital gives excellent results and enables control of the microbiological quality of DUWL water in the long term.