Molecular methods are increasingly applied for virus detection in environmental samples without rendering data on viral infectivity. Infectivity data are important for assessing public health risks from exposure to human pathogenic viruses in the environment. Here, treatment efficiencies of three (drinking) water treatment processes were estimated by quantification of the indicator virus bacteriophage MS2 with culture and real-time reverse transcription polymerase chain reaction (qRT–PCR). We studied the virus reduction by slow sand filtration at a pilot plant. No decay of MS2 RNA was observed, whereas infectious MS2 particles were inactivated at a rate of 0.1 day−1. Removal of MS2 RNA and infectious MS2 particles was 1.2 and 1.6 log10-units, respectively. Virus reduction by UV and gamma irradiation was determined in laboratory-scale experiments. The reduction of MS2 RNA based on qRT–PCR data was negligible. Reduction of infectious MS2 particles was estimated at 3.0–3.6 log10-units (UV dose up to 400 or 800 J/m2) and 4.7–7 log10-units (gamma dose up to 200 Gray). As shown in this study, estimations of viral reduction, both inactivation and removal, obtained by molecular methods should be interpreted carefully when considering treatment options to provide virus-safe drinking water. Combining culture-based methods with molecular methods may provide supplementary information on mechanisms of virus reduction.