This study was designed to analyze the bacterial composition of the Oreochromis niloticus and the impact of its surrounding water. Nile tilapia fish samples were obtained from two Northern Delta lakes in Egypt Manzala and Borollus. DNA was extracted, and the bacterial communities in the stomach content, were classified (to family and species levels) using the 16S rRNA-based analysis. 1,426,740 amplicon sequence reads corresponding to 508 total operational taxonomic units were obtained from the two metagenomics libraries in this study. The Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes were the most dominant bacterial phyla in all samples. A total of 36 different classes and 132 families were identified, many of which had shared presence in all samples, while others were exclusive to the other sample. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. We observed a notable difference between gut bacteria of Nile tilapia fish obtained from Lake Borollus and Lake Manzala. There is a remarkable indication that Nile tilapia fish living in Lakes Borollus is heavily burdened with pathogenic microbes most notably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This finding was also congruent with the functional prediction from the metagenomic data implying that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The results obtained indicate a strong influence of the host environment on the composition of its microbiota. Knowing the structure of the microbiome is the first step toward exploring the proper management of this ornamental fish in captivity.