Vibrio alginolyticus, Vibrio chlorea, and Enterococcus cloacae were the main bacterial pathogens investigated during recurrent episodes of mortalities among farmed flathead grey mullet (Mugil cephalus) in the Bahar El-Baqar area, Sharqia governorate, Egypt, during the summer season in 2021. Nevertheless, the contamination of water with heavy metals was evaluated. In this study, a total number of sixty moribund and freshly dead Mugil cephalus were examined clinically and upon post-mortem. Then, the bacterial isolates were subjected to bacteriological phenotypic examination, 16S rRNA gene sequencing, and antibiotic sensitivity testing. Histopathological screening and the immunity response of naturally infected M. cephalus were also implemented. In areas where bacterial strains were recovered in a high percentage, water contamination with Cu, Fe, and Ni was higher than the permissible limit. The results showed a high similarity (99–100%) to Vibrio and E. cloacae strains using phylogenetic analysis of 16S rRNA. Most isolates exhibited sensitivity to florfenicol, ciprofloxacin, and norfloxacin, while they were resistant to erythromycin and amoxicillin. Hemorrhage, oedema, hemosiderosis, and melanomacrophage activation in most affected tissues of infected M. cephalus were detected by light microscopy. Nevertheless, higher levels of AST and ALT, as well as serum inflammatory markers, CRP, and lysozyme activity, were shown in infected fish. There were higher MDA levels, along with a reduction of GSH, SOD, and catalase, in the gills and brain of infected M. cephalus, compared to the control fish. Our obtained data confirmed the high prevalence of Vibrio serovars and E. cloacae in infected grey mullets, describing their histopathological alterations, higher inflammatory response, and oxidative stress impact. These results could be useful indicators for understanding the pathogenesis of these pathogens in correlation with water parameter deterioration. Thus, the emergence of Vibrio and E. cloacae species in this study threatens the brackish water aquaculture industry in Egypt and poses a public health concern.