Abstract: This study was carried out on Lake Qarun, Fayoum Province, Egypt throughout four seasons, spring 2004 to winter 2005. The concentration of Zn in water as well as in fish organs was always higher than Cu. Correlations between concentration of heavy metals in water and fish organs were elucidated. The concentrations of heavy metals in fish samples indicated that Tilapia zillii were higher than those of Mugil cephalus, which is attributed to their feeding behavior. It was found that these metals have been accumulated in fish organs in different concentrations, which were much higher, several times in some cases, than those found in the surrounding water. The analysis of variance (ANOVA, 1-way analysis) for heavy metals in water and fish organs indicated significant difference. Bioaccumulation factor values showed that the trend of accumulation of metals in fish organs was apparent in liver, gills and muscle, respectively. Lesions deformations were detected and analyzed to clarify the possible role of water pollution on the efficiency of fish and hence the declining fish production of Lake Qarun. The results suggest that the Lake Qarun system is contaminated with heavy metals and the consumption of fishes of the Lake could pose health damage to the local population whose diet consists mainly of fish. A recommendation is given to rescue Lake Qarun from these serious ecological problems.