Dental unit waterlines may be heavily contaminated with microorganisms and are a potential source of infection for both practicing staff and immunocompromised patients. Contamination of dental unit water lines can be inhibited with the use of disinfectants. Objective: The objective of this study was to evaluate and compare the efficacy of commercially available Aloe Vera, 3% sodium hypochlorite (NaOCl), and 5gms sodium dichloroisocynurate (NaDCC) in controlling microbial contamination of dental unit water systems. Materials and Methods: Fifteen dental units, divided into 3groups, were selected for the study. Water samples were collected from the outlet of air/water syringe and high speed hand piece and base line samples were obtained. 500ml of three disinfectants were added to the reservoir bottle. Their efficacy was assessed by the total viable count (TVC) method, after 40 hours, one week and three weeks post disinfection, and was statistically analyzed using one way Anova and wilcoxon signed rank test and post hoc analysis. Results: NaDCC was found to be the most effective in reducing the microbial colonies, with 99.9% reduction at 40 hours and 100% reduction in mean CFU/ml at 3-week interval of disinfection as compared to sodium hypochlorite and aloevera which was statistically significant (p=0.005). Conclusions: Decontamination protocol should be followed in order to minimize the risk of exposure to potential pathogens from dental units. Chemical-based disinfectants such as NaDCC can be considered effective, fast acting and economical for treating microbial contamination in dental unit waterlines.