Heavy metals (HMs) have attracted global attention due to their toxicity, persistence, and accumulation in aquatic fish in the polluted water environment. The consumption of these fishes exposed humans to a higher risk of non-carcinogenic and carcinogenic risks. In this study, we provided a critical overview of the potential sources and concentration of HMs in Nigeria’s freshwater. Furthermore, we reported their pollution level in widely eaten fish species in the country. Our findings show that effluent from anthropogenic and industrial activities is one of the major sources HMs in the country. The mean concentration of Zn (9.02 mg/L), As (7.25 mg/L), Cu (4.35 mg/L), Fe (1.77 mg/L), and Pb (1.46 mg/L) in Nigeria’s freshwaters were found to be high than Nigerian Standard for Drinking Water Quality permissible limit. This study demonstrated considerable health risks associated HMs via dietary consumption of different fishes from polluted waters. Therefore, we recommended an urgent need for effective management HMs in water bodies in order to protect the lives of people living in the country.