The use of advanced oxidation processes (AOP) are expected to increase for removal of emerging contaminants and pathogens from drinking water. In this study, the performance of a small community ultraviolet light reactor in combination with hydrogen peroxide (H2O2) for MS2 coliphage inactivation with two different flow rate conditions of 1 gal/min (gpm) and 2 gpm was evaluated. Following UV radiation, MS2 showed a reduction of 5.3-5.8 log10 when quantified with cultural plaque counts, whereas corresponding quantitative polymerase chain reaction (qPCR) data showed only a 1.7-2.8 log10 reduction in viral RNA copy number. When H2O2 was added at either 2.5 or 5 ppm with UV at both flow rate conditions, enhanced MS2 inactivation occurred with a more than 7 log10 reduction observed via plaque counts, indicating that all added MS2 had been inactivated, since no plaques were formed after incubation at 37 °C for 24 h. In contrast, qPCR only showed a corresponding 3-4 log10 reduction in viral RNA copy number. This research also sheds light on the inactivation of MS2 with ultraviolet light and in the presence of hydroxyl radicals and provides a practical use of qPCR to detect MS2 concentration following advanced oxidation relative to traditional plaque methodology; however qPCR detection overestimates the true number of infective virus.