A method and system flows water through a water system in proximity to an ion generation device and to a source of ultraviolet (UV) radiation that combines photochemistry principles, heavy metal toxicity, and UV light radiation to form a highly effective combined water disinfection process. Using ion generation and UV irradiation, the method and system synergistically improves the disinfection and bactericidal effects of ion generation or UV radiation working individually by making ion-exposed microorganisms more susceptible and less resistant to the bactericidal effects of UV radiation. The combined method and system of the present invention may include control means such that the method and system can be configured for single pass through, dual pass through or for recirculation such that the order of exposure to the ion generation and UV radiation aspects can be varied or altered. The method and system of the present invention may also be provided with means for controlling the system flow rate, ion generation and UV radiation levels to maximize performance, to minimize energy consumption, and, in some situations, to selectively target certain microorganisms for inactivation.