Ultraviolet light-emitting diodes (UV LEDs) have shown ability to inactivate microorganisms and viruses in water. The unique characteristic of the UV-LEDs' diversity in wavelengths ranging from UV-C, UV-B, and UV-A, allows for wavelengths to be combined in different manners for polychromatic irradiation. Previous studies reported no synergy from simultaneous or sequential UV-C and UV-B as well as UV-C or UV-B followed by UV-A irradiation. However, synergy was reported for UV-A followed by UV-C or UV-B irradiation on various microorganisms. Nevertheless, no clear ground has been reached on whether to adopt single UV-C wavelengths or UV-A followed by UV-C LED, irradiation on inactivation of microorganisms and viruses in water. Therefore, this work evaluates the disinfection efficacy of single UV-C as well as UV-A followed by UV-C LED irradiation on Escherichia coli, Bacillus spizizenii spores and MS2 bacteriophage in water. The UV-C wavelengths were represented by 267 and 278 nm UV LEDs, and UV-A by 368 nm UV LEDs. In this study, E. coli was highly susceptible to UV radiation followed by B. spizizenii spores, and lastly MS2. Repair following UV inactivation was only observed in E. coli. The synergistic effect found in both E. coli, and B. spizizenii spores was attributed to the different inactivation mechanisms of the UV-C and UV-A wavelengths. In both single UV-C, and UV-A followed by UV-C LED irradiations, single 267 nm UV-C LED showed higher inactivation efficacy. Meanwhile, single 278 nm UV-C LED showed higher efficacy in terms of suppression of repair, and electrical energy consumption. Using single UV-C LEDs in a water disinfection system cuts down on related extra costs by avoiding combined wavelengths while still attaining better levels of microorganism inactivation, repair suppression and electrical energy consumption. These findings are applicable for the design and implementation of UV LED water disinfection systems.