The present study aims to investigate some heavy metal concentrations in water and fish organs (liver, gills and muscle) of Oreochromis niloticus and Clarias gariepinus in Edku and Burullus lakes. In addition, estimate pollution indices such as Pollution index (PI), heavy metal evaluation index (HEI), contamination index (Cd), and its potential health risk assessment (HQdermal). Also, the health risks from fish muscle consumption (THQS) and Bioconcentration factor (BCF). Heavy metals concentrations in water were found in the following order Fe > Zn > Mn > Pb > Cd in Burullus lake, whereas they follow the order of Fe > Mn > Pb > Zn > Cd in Edku lake. Where, Edku lake ranked as second after Burullus lake in accumulation of metals (Mn, Zn, Pb) with slightly increasing in concentrations of Fe and Cd. For, the same heavy metals in fish organs of the two examined species in Burullus and Edku lakes had the order: Fe> Zn> Mn> Pb> Cd and the residues of all investigated heavy metals in liver and gills of the both examined fish species were much higher than that in their muscles. The pollution indices showed that both lake's water is highly contaminated based on PI, HEI and Cd. where PI average values of Fe and Cd were higher in Edku lake than Burullus lake. While, PI average values for Mn, Zn and Pb were higher in Burullus lake than Edku lake. Values of HQdermal, THQS and their HI were lower than 1 for all heavy metals from all sites in both lakes during the study seasons. From the above results, it's concluded that the two lakes suffer from different types of pollution and the control of this pollution depends on the treatment of sewage, agricultural and industrial wastes before dumping into these lakes.