Heavy metal concentrations and magnetic susceptibility of sediment samples were analyzed as indicators of urban and industrial contamination in Anzali wetland in Gilan, Iran. The aim was to investigate the suitability of magnetic properties measurements for indicating heavy metal pollution. The concentration of six heavy metals (Ni, Cr, Cd, Zn, Fe, and Pb) was determined in different depths of four sediment core samples within four different regions of the wetland (Abkenar, Hendekhaleh, Shijan and Siakeshim). Average concentration of heavy metals in the sediment cores was higher than the severe effect level (SEL) for Ni, Cr and Fe (77.26, 113.63 ppm and 5.2%, respectively) and lower than SEL for Cd, Zn and Pb (0.84, 137.7, 29.77 ppm, respectively). It was found that the trend of metal concentrations with the depth is different in each core and is related to the pollution discharges into the rivers entering the wetland. Core magnetic susceptibility measurements also showed different magnetic properties in each core. Cluster analysis was applied using Pearson correlation coefficient between heavy metal concentrations and magnetic properties across each core. Significant relationship was found to exist between magnetic susceptibility and the concentration of Ni in Abkenar and the concentration of Fe in other regions. Whereas Abkenar is almost the isolated and uncontaminated region of the wetland, it revealed a difference in magnetic properties between contaminated and uncontaminated sediments. It was concluded that magnetic properties of samples from contaminated zone were mostly related to Fe content. The result of this study demonstrated that magnetic susceptibility measurements could be applied as a proxy method for heavy metal pollution determination in marine environments in Iran especially as a rapid and cost-effective introductory site assessments.