Amirkola (more than 500 years in age), Kiashahr and Zibakenar (a few decades in age) lagoons are located on the Sefidrud Delta, the southern coast of the Caspian Sea. Evaluating the pollution degree caused by heavy metals (including Cu, Cr, Co, Ni, Pb, Zn and V), 106 sediment samples and three sediment cores were taken from studied lagoons. Three indices, including geo-accumulation index (Igeo), contamination factor (CF), and pollution load index (PLI), were employed to determine the contamination degree in the lagoons. Based on contamination indices, the Kiashahr and Zibakenar lagoons show significant to moderate contamination with Co, Cu, Pb, Zn and V. Nonparametric statistical analysis (Two-step cluster analysis, analysis of variance, and T-test technique) was used to discriminate the pollution sources. Statistical methods indicated the unique interpretation of contaminants sources. There is a significant difference in metal concentrations between Amirkola and two younger lagoons. Despite the same geogenic origin of sediments in the Sefidrud Delta and lagoons deposits, Co, Zn, and Pb show anthropogenic sources in the newly-formed Kiashahr and Zibakenar lagoons.