This study explored the applicability of using TaqMan qPCR (quantitative polymerase chain reaction) for Escherichia coli, Salmonella enterica and non-virulent Vibrio cholerae detection in surface and drinking water. One hundred and twenty water samples were collected monthly (January 2017–December 2017) from the surface water (input) and drinking water (output and distribution networks) of two drinking water treatment plants (DWTPs) in Damietta County, Egypt. The distribution of the studied bacteria based on their detection by TaqMan qPCR compared with membrane filtration (MF) technique showed that the higher positive samples were detected by TaqMan qPCR. The bacterial count was totally absent in all output samples. TaqMan qPCR assay (based on sequence detection of uidA, invA, and ompW) revealed 97.96%, 99.14%, and 98.3% specificity for E. coli, S. enterica, and non-virulent V. cholerae, respectively, compared with 100% specificity for all strains when MF cultures were applied. TaqMan qPCR exhibited 100% sensitivity for all strains, while it was 91.67%, 80%, and 50% using MF cultures for E. coli, S. enterica, and non-virulent V. cholerae, respectively. In conclusion, TaqMan qPCR sensitivity makes it a useful tool for urgent fast monitoring of water contamination, especially in network samples that contain low bacterial count.