Viral indicators were used to evaluate the effectiveness of water treatment processes and to determine the source of faecal pollution with a view to promote water source management. Water samples were collected from three critical points of the Temba, Klipdrift and Wallmansthal water treatment plants (raw water, settled water and filtered water). The viral indicator concentrations and selected physicochemical parameters were measured using standard methods. Random water samples were subjected to real-time polymerase chain reaction analyses. Subsequent to filtration, the removal efficiency of the three Waterworks was recorded as follows: 93.2, 96.1 and 95.7 % for somatic coliphages, respectively; and 69.4 and 68.4 % FRNA coliphages for Temba and Klipdrift. There was a notable 50 % reappearance of FRNA coliphages in filtered water samples from Wallmansthal. Positive correlations were observed between the physicochemical parameters and somatic coliphages, with the exception of the pH and the temperature in Wallmansthal. Both turbidity and temperature indicated positive correlations with FRNA counts from Temba and Klipdrift. Negative correlations were observed between all the physicochemical parameters and FRNA counts from Wallmansthal. The real-time polymerase chain reaction analyses revealed the persistence of GA genotype FRNA (Group II, which is of human faecal origin) in all the water samples. The MS2 genotype (Group I) and Qβ genotype (Group III) FRNA, which are of animal origin, were detected only in the raw water from Temba. Efforts should be focused on the protection of water sources and the optimisation of treatment processes in order to prevent viral persistence during water treatment.