Lake Manzalah is economically the most important Delta lake in northern part of Egypt, but Lake Bardawil is the least polluted wetland in Egypt as it is considered as a protected area. In the present study, a comparative study on the both lakes and on the pollution effect were done accompanied by histological and histochemical investigations on gonads (testes and ovaries) of Liza ramada and Dicentrarchus labrax which are inhabiting the both lakes. In conclusion, the results revealed that there were accumulated heavy metals in the gonads of the two studied fishes which implies the bad effects of the toxic heavy metals which disrupt and impair their reproduction process. These findings recommended that improved water quality control and periodically environmental monitoring are necessary. Recommendations from the health authorities for regarding the acceptable number of fish meals from Lake Manzalah, Egypt to be consumed weekly should be obeyed by the fish consumers.