Objective <p>This study aims to determine the optimal disinfection frequency by comparing the effectiveness of different hydrogen peroxide (H₂O₂₎ shock treatment schedules in controlling contamination of dental unit waterlines (DUWLs).</p> Methods <p>Three dental units were randomly assigned to groups A, B, and C. After initial treatment with the Biofilm-Removing Set (BRS^®), continuous treatment with 0.0141% H₂O₂ was applied. Shock treatment with 1.41% H₂O₂ was conducted every three weeks for group A, every 2 weeks for group B, and weekly for group C over 6 weeks. Water samples were collected thrice weekly to monitor bacterial counts, with a compliance threshold of 100 CFU/mL. Electron microscopy was used to assess biofilm morphology.</p> Results <p>A total of 132 samples were analyzed. Following BRS^® treatment, bacterial counts decreased significantly to 15–45 CFU/mL. Groups B and C achieved 100% compliance, while group A had 68.42% compliance, with visible biofilm noted. There were significant statistical differences in compliance rates among three groups (<i>p</i> &lt; 0.05).</p> Conclusions <p>Continuous treatment with 0.0141% H₂O₂, combined with biweekly or weekly 1.41% H₂O₂ shock treatment, may help control DUWLs contamination in the short term under the conditions tested. Future studies should expand the sample size and duration for long-term efficacy assessment.</p>