Background & Aims of the Study: The present research aims to use sediment quality indices in the assessment of toxicity and ecological risk factors of heavy metals Pb, Cu and Zn in Anzali, Meighan, Shadegan and Hashilan wetlands. Material & Methods: Given the environmental conditions, surface sediments in 71 diverse stations were sampled in three replications. Having preparation and subjected to acid digestion of sediment samples, 0.5 g of each sample was digested with a mixture of nitric acid and super-pure ratio of 4 to 1 perchloric acid. Finally the concentration of these metals was determined using the contrAA 700 Analytic Jena Atomic absorption spectroscopy. Results: The results of the potential acute toxicity and the ecological risk of the considered metals indicated low toxicity and risk. Also, the outcomes of Modified Hazard Quotient (mHQ) indicated a low to moderate pollution risk in Anzali wetland, very low pollution in Shadegan wetland, and in Meighan wetland for Pb and Cu, low pollution to very low and for Zn metal it showed low to high pollution. In Hashilan wetland Modified Hazard Quotient for Pb and Zn showed very low pollution and for Cu it was negligible to moderate among others. Conclusion: However, the growth of urbanization and the increase of various anthropogenic activities such as agriculture, urban, industrial ... within the wetland basin (draining area) and entry of untreated urban and rural sewage requires urgently continuous monitoring of wetlands as well as the assessment of their health risks and ecological risk among others.