Water in dental unit waterlines (DUWL) represents a risk for vulnerable patients if its microbiological quality is not controlled. The aim of this prospective study was to evaluate two systems for its management under real conditions: Hygowater® and IGN Calbenium®. Samples of the output water of DUWL were obtained for 5 previously contaminated units connected to Hygowater®, and 5 non-contaminated units connected to IGN Calbenium®, which was already effective for more than 1 year, as a control group. Samples were regularly collected up to 6 months after the implementation of Hygowater®, and were then cultured and analyzed. With IGN Calbenium®, except for a technical problem and a sample result in one unit at 6 months (Heterotrophic Plate Count (HPC) at 37 °C of 66 colony forming units (cfu)/mL), the results showed an absence of contamination. Hygowater® took a couple of weeks to be effective on initially contaminated DUWL (over 200 cfu/mL for all the units), then showed its efficacy for 2 months (HPC at 37 °C with a mean of 40.2 ufc/mL, and HPC at 22 °C with a mean of 0.2 ufc/mL). At 6 months, results were satisfactory for HPC at 22 °C (mean of 12 ufc/mL), but HPC at 37 °C gave non-satisfactory results for 4 of the 5 units (mean of 92.2 ufc/mL). Both systems have an effect on the microbiological quality of DUWL. IGN Calbenium® appears to be more reliable on a long-term basis.