Abstract: In the present report, we have determined the gonadal free amino acid compositions in Oreochromis niloticus collected from three sites in Lake Mariut: SE basin (less polluted), main basin (moderately polluted) and SW basin (highly polluted), in an attempt to develop sensitive biomarker to evaluate pollution effects from multiple sources. Variations of free amino acids (FAAs) were apparent in the polluted sites; total FAAs in testes and ovaries exhibited significant increases as compared to the less polluted site. This increase was attributed to increases in all individual amino acids including essential and non-essential ones. ANOVA indicated significant changes in all testicular FAAs, excluding phenylalanine. Levels of non-essential amino acids showed obvious alterations in ovaries. However, the increase in most essential amino acids, although insignificant, yet it was quite observable. In addition, the ratio of essential to non-essential amino acids was insignificantly decreased in gonads. This may be indicative of changes in protein metabolism.