Many commercial dental unit waterline cleaners are available. Results regarding the efficacy of these products vary and sampling methods and laboratory procedures can affect results. This study was conducted to test the efficacy of a continuous-use stabilized chlorine dioxide product and determine if two different sampling methods produced the same results. There was a statistically significant difference between the treated units and the control units (p < 0.05) but the two sampling methods revealed no statistically significant difference (p > 0.5). Treated units showed a decline in the mean number of colony forming units per milliliter (CFU/mL) over the study period but the level was not consistently low enough to meet the ADA-recommended levels of 200 CFU/mL. The findings of this study indicate that it is not necessary to replace a continuous use product with fresh, untreated water when testing water quality.