Wetlands are highly sensitive to pollution effects as they are usually low lands in comparison to the surroundings. Consequently, pollution with heavy metals in the wetlands ecosystems may have changed the ecosystem's biogeochemistry. Gomishan and Zarivar wetlands are regarded as two of the most important wetland regions in south eastern corner of Caspian Sea and in Western Iran respectively. We report the results from a detailed research based on two metals (Pb and Cd) measured in muscle of two fish species (Cyprinus carpio and Liza saliens) from Gomishan and Zarivar wetlands. Twenty three leaping mullet (Liza saliens) fish samples (from the 9 stations) and twenty common carp (Cyprinus carpio) were collected in year 2013 from Gomishan international wetland and Zarivar wetland respectively. Using a hot-block digester, the muscle samples were digested with a combination of perchloric acid (HCLO4) and nitric acid (HNO3) and then examined by atomic absorption spectrophotometry. The ranges of the concentrations of metals in the edible muscle tissues were: Pb 0.14–0.57 μg/g; Cd 0.34–0.49 μg/g; in common carp and Pb 0.00075–0.03 μg/g; Cd; 0.08–0.025 μg/g in leaping mullet. Pb and Cd concentrations between both fish species were statistically significant (insert the p value). There was no statistically significant correlation between the metal concentration of the muscles and the fish weight for both species. The concentrations of heavy metals in muscle of examined both fish species were below the permissible levels and should not pose health problems for human consumption. Periodic monitoring of these metals in both fishes and water to ensure safety is recommended.