In this study, chlorine dioxide (ClO2) was used as an alternative disinfectant with vanillic acid, p-hydroxybenzoic acid, and humic acid as the organic precursors in a natural aquatic environment. The primary disinfection by-products (DBPs) formed were trihalomethanes (THMs) and haloacetic acids (HAAs). Under neutral conditions (pH = 7) for vanillic acid, more total haloacetic acids (THAAs) than total trihalomethanes (TTHMs) were found, with a substantial increase during the later stages of the reaction. In the case of p-hydroxybenzoic acid, the amount of THAAs produced was minimal. Raising the concentration of ClO2 was not favorable for the control of THAAs in low concentrations of vanillic acid. ClO2 could reduce the total amount of TTHMs and THAAs for higher concentration of vanillic acid. It was found that the humic acid treatment dosage was not significant. Under alkaline conditions (pH = 9), the control of TTHMs and THAAs for the treatment of vanillic acid was better and more economical, however, an appreciable amount of inorganic by-products were observed. Under the same alkaline condition, the control of THAA for the treatment of p-hydroxybenzoic acid was not beneficial and for the treatment of humic acid was not significant.