Research on microorganism reduction by physicochemical water treatment is often carried out under the assumption that the microbiological enumeration techniques are not affected by the presence of coagulants. Data presented here indicate that bacteriophage enumeration by plaque assay and RT-qPCR (reverse transcription quantitative polymerase chain reaction) can be affected by these water treatment chemicals. Treatment of water samples with an alkaline protein-rich solution prior to plaque assay and optimization of RNA extraction for RT-qPCR were implemented to minimize the interference. The improved procedures were used in order to investigate reduction of three viral pathogens and the MS2 model virus in the presence of three coagulants. A conventional aluminium coagulant was compared to alternative agents (zirconium and chitosan) in a coagulation-filtration system. The highest virus reduction, i.e., 99.9–99.99%, was provided by chitosan, while aluminium and zirconium reduced virus by 99.9% in colour-rich water and by 90% in water with less colour, implying an effect of coagulant type and raw water quality on virus reduction. Although charge characteristics of viruses were associated with virus reduction, the results reveal that the MS2 phage is a suitable model for aggregation and retention of the selected pathogens.