This study was performed with aims to determine the concentration of lead, nickel and mercury in muscle of three species of Boleophthalmus dussumieri, Sardinella melanura and Otolithes ruber in Khor Mousa area in summer of 2013. Water sampling was performed from intervals of 0, 150, 300, 450 and 600 meters from the output effluent of Bandar Imam petrochemical factory in triplicate. Compound sample it was prepared with 30 numbers of each species at the nearest of outlet. Muscle tissue isolated and with wet method digested and then its heavy metals was analyzed by using atomic absorption. The results of experiment showed that mean concentration of Pb, Ni and Hg in water samples were respectively 76.98, 168.72 and 0.873 µg/lit, that the concentration of Hg was exceeded from the normal range by the WHO (World Health Organization) standard. According to the test results in muscle tissue, mean concentration of Pb was respectively 632±2.52, 441±7.34 and 389±7.94 µg/kg dry mater and Hg was respectively 9.91±0.58, 19.5±2.93 and 47.1±1.48 µg/kg dry mater, that these concentrations were less than the standard limit of WHO and FDA (Food and Drug Administration). Also, the concentration of Ni was determined respectively 497±7.234, 602±4.16 and 972±8.14 µg/kg dry mater that was more than the standard limit of WHO.