Abstract Objective: To compare the effect of disinfection of dental unit waterlines (DUWLs) on bacterial load using disinfection methods and agents like 0.12% chlorhexidine gluconate (CHX), time-dependent flushing (1 min, 2 min), and using distilled water and tap water as water sources. Materials and Methods: Four dental units were taken: Unit A contained 0.12% CHX, Unit B contained distilled water, Unit C contained tap water, and Unit D included flushing for 1 and 2 min. A total of 36 water samples were collected in 2 weeks. One sample of tap water from basin was taken as study control. One sample each from Unit A, B, and C and 2 samples from Unit D (1 min and 2 min flushing) were taken as baseline samples. Samples were collected three times a week and assessed for total viable count (TVC) and types of organisms present. Results: For Unit A, no growth of microorganisms was observed. Flushing for 1 min and 2 min showed variable TVC. No significant difference was seen in TVC of units B, C, and D in comparison to the baseline samples. Conclusions: It was found that 0.12% CHX was very effective in controlling DUWL contamination. Adhering to a recommended 2 min flushing regimen can reduce the bacterial counts, but is not a reliable means of disinfection.