Increased water body contamination by heavy metals (HMs) is a serious health hazard to both aquatic biota and their predators. The degree of contamination is a function of bioavailability and bioaffinity to an organism. Metallothioneins (MTs) –a protein with high metal binding ability was used to assess the differential bioaccumulation of HMs in liver and skeletal muscles of Tilapia Zilli. HM concentration in all the liquid habitats was above the permissible limits of Federal Ministry of Environment with Zinc having the highest concentration ranging from 6.791-11.825 ppm. Exposure of T. Zilli to the three liquid habitats for 72 hours with sample collection twenty-four (24) hourly showed significant (P ≥ 0.05) induction of MTs by HMs accumulated in liver and skeletal muscle tissues of T. Zilli exposed to test habitats. Fishes showed higher induction in the downstream liquid habitat, where accumulation of HMs was higher in liver than muscle tissues. Fishes exposed to that habitat recorded MT concentrations of 102.859µg/g WWt and 83.947µg/g WWt after 72 hours of exposure for liver and skeletal muscle respectively. The liver demonstrated higher bioaccumulation potential than muscle tissues and the highest bioaccumulation factor for most of the HM was associated with the downstream habitat. T. Zilli from this study bioaccumulated HM and MTs played a vital role bioaccumulation assessment of HM. Though HM in skeletal muscles were relatively low, it still poses health threat through bioaccumulation. Thus, consumption of fish from polluted bodies needs to be avoided.