This study aims to study the diversity of bacteria in different water samples which taken from Meet Faris drinking water station, during the period from July, 2013 till June, 2014. The bacteriological analyses involved total bacterial counts (TBCs), total coliforms (TC) and estimation of fecal coliforms (FC), fecal streptococci and pathogenic bacteria. Fifty pathogenic bacterial isolates obtained from raw water samples. The most prevalent organisms were E.coli (30%), Klebsiella.spp (14%), Pseudomonasspp(16%), Proteus. Spp (10%), E. fecalis (14%) Shigellaspp.(8%), Staph.coccus (8%). According to antibiotic susceptibility test results, enrofloxacin and gentamicin were the most effective antibiotic on E.coli isolates. The obtained results revealed that, the River Nile water was subjected to sewage pollution. Detection of E.coli by PCR was found to be important for confirmation of the detected E.coli isolates.