Pollution of Lake Qarun with heavy metals has become a more serious concern during recent years as it affects the physicochemical characteristics of the water, sediments and biological components and may damage aquatic organisms as well. Lake Qarun receives the agricultural and sewage wastewater loaded with heavy metals through two main drains; El-Batts and El-Wadi.  Therefore, an annual increase in the accumulation of pollutants and heavy metals has been detected in all its components (e.g. water, sediment and fish). The present study aimed to evaluate the seasonal variation of heavy metals' contents (Fe, Cu, Zn, Cd, Pb and Ni) in water and the bioaccumulation factor of these heavy metals in Solea aegyptiaca fish samples, collected from Lake Qarun. Thus, information was provided regarding histological changes in gills, liver and muscle organs. This study was carried out along Lake Qarun at four sites (Eastern, Southern, Northern and Western) during the winter and summer seasons, 2019. The results revealed that summer was higher in heavy metal concentration in water than winter. Additionally, the eastern and southern sectors showed increased water concentration of heavy metals. Concerning fish samples, the present study exhibited that, the maximum values of bioaccumulation factor were recorded in the gills and liver, whereas the minimum values were observed in the muscles. The gills of Solea aegyptiaca accumulate higher levels of Zn, pb and Ni, while, Fe, Cu and Cd accumulated mainly in the liver. Results showed obvious histopathological alternations and clear damage in gills, liver and muscles of Solea aegyptiaca collected from the eastern and southern sectors of Lake Qarun.