The invasion of fish by heavy metals is a recognized environmental problem. Heavy metals, after leaking into the water, penetrate fish directly through the gill and later the skin. Fish develops protective defense mechanisms against the damaging effects of heavy metals. This study was aimed to investigate the concentrations of certain metals (cadmium, iron, manganese, cobalt, and lead) in the muscle tissues of the Nile tilapia (Oreochromis niloticus) and their possible impact on its histological, nanomechanical, and biochemical biomarkers. The results showed that fish muscle from the polluted site contained high levels of heavy metals compared to the reference site. Biochemical profile of the Nile tilapia showed that serum glucose, total proteins, uric acid, creatinine, bilirubin, superoxide dismutase, and malondialdehyde were elevated in exposed tilapia compared to their corresponding reference. Histological examination of the liver showed severe alterations in the liver tissue. Nanomechanical properties (roughness and stiffness) confirmed the damaging effect of metals on the liver tissue. These findings provide a rational application of histological, nanomechanical and biochemical parameters to be used as indicators of metal stress. Integrated biomarker response is a comprehensive index of all biomarkers and a good indicator of the health status of aquatic ecosystem.