In this study water samples of different origins (subalpine lake, artificial lake and river) were treated by pre-oxidation, coagulation/flocculation, adsorption on granular activated carbon and disinfection. Different laboratory-scale tests were carried out to evaluate the treatment impact on ClO2 consumption in disinfection and on the formation of disinfection by-products (trihalomethanes, adsorbable organic halogen, chlorite and chlorate). The results showed that coagulation/flocculation and activated carbon adsorption have the most significant impact on reducing disinfectant consumption. Pre-oxidation of artificial lake water with KMnO4 and NaClO determines the highest ClO2 consumption. Regardless of the water source, the amount of chlorite produced after disinfection with ClO2 is 40–60% lower using NaClO as the pre-oxidant rather than KMnO4 or ClO2. Otherwise, NaClO leads to a high formation of adsorbable organic halogens and trihalomethanes in artificial lake water (up to 60 μg/L and 20 μg/L respectively), while in the case of ClO2 oxidation, trihalomethane formation is 98% less compared to NaClO. Further, adding ferrous ion in coagulation/flocculation improves the removal of chlorite produced during pre-oxidation, with a 90% removal, mainly due to the reduction of chlorite to chloride. Finally, activated carbon adsorption after pre-oxidation and coagulation/flocculation removes adsorbable organic halogens and trihalomethanes respectively by 50–60% and 30–98%, and completes the chlorite and chlorate removal.