For identifying fecal pollution in water, microbial indicators, particularly those from the coliform groups Escherichia coli and Enterococci, have been utilized, which are considered guidelines for the quality of drinking water. The multiple-tube fermentation (MTF) and membrane filter (MF) procedures for detecting indicator organisms are recognized conventional methods, and they are compared with the multiplex PCR method. Three sets of different primers were used in combination with the multiplex PCR procedure. The first set aims to amplify 876 base pairs from the lacZ gene, which is present in all coliform bacteria, including E. coli. The second set aims to amplify 147 base pairs from the uidA gene, which is unique to E. coli. While the final set yields a tuf gene with 112 base pairs that are unique to all Enterococci. The multiplex PCR technique has been found to be an effective, sensitive, and quick method for detecting these three microbial indicators in contaminated water. In Damietta County, Egypt, three water treatment stations (El-Rahmna - El-Adlyia - El-Bostan) were evaluated for their effectiveness at removing pollutants from the water using the optimized multiplex PCR.