To explore the antibacterial activities of Allium sativium (garlic) extract was tested against two waterborne pathogenic strains isolated from River Nile, to mitigate the increase of bacterial resistance to conventional antibiotics. The two isolates were identified as Enterobacter cloacae DSM 3264 BRB & Enterobacter cloacae MB11506_1CHB by MALDI-Tof-MS. Aqueous, methanolic and oil extraction of garlic were tested for their inhibitory activity against the selected strains using well diffusion method. Enterobacter sp. were more sensitive towards oil extract with inhibition zone 2.3 cm rather than aqueous and methanolic extractions with was 50%. Analysis of garlic essential oil by GC-MS dedicated six sulfur compounds represented 25% of total detected compounds in the oil.