Monitoring heavy metal accumulation is essential for assessing the viability of aquatic ecosystems. Our methodology involved integrating analysis of immunological, stress, inflammatory, and growth-related gene expression in male and female Nile tilapia with on-site recordings of physicochemical parameters. Additionally, we assessed the effect of different physicochemical parameters on heavy metal bioavailability and residual concentration in fish and water. Samples of fish and water were gathered from three different localities: Lake Brullus, a brackish lake sited in northern Egypt; Lake Nasser, an artificial freshwater reservoir located in southern Egypt; and El-Qanater El-Khayria, a middle-freshwater location belonging to the Rashid branch of the river Nile. The assessment of heavy metal residues (Fe, Cu, Zn, Mn, and Ni) revealed that their concentrations were higher in fish specimens compared to their counterparts in water (except for Ni). In addition, Lake Brullus emerges as the most polluted area, exhibiting elevated levels of heavy metals concentrations in water and fish specimens. In contrast, Lake Nasser showed the least degree of heavy metals pollution. Gene expression analysis revealed gender-specific responses to heavy metal exposure at the three investigated water bodies. The expression of hepatic antioxidant genes (GST and MT) and inflammatory-related genes (CC-chemokine and TNFα) increased in males compared to females. In females, the immune and pro-inflammatory-related genes (IgM and CXC2-chemokine) transcripts were upregulated. Additionally, growth-related genes were downregulated in both Lake Brullus and El-Qanater; on the contrary, fish samples from Lake Nasser exhibited a normal expression pattern of growth-related genes. Stress-related genes (HSP70 and HSP27) showed significant downregulation in gills of both genders from Lake Brullus. The minimal presence of heavy metal contaminants in Lake Nasser seems to endorse the normal patterns of gene expression across all gene categories. A potential gender-specific gene expression response towards pollution was noticed in genes associated with inflammation and antioxidant activities. This highlights the importance of considering gender-related responses in future environmental assessments.