The aim of the present study was to determine zinc (Zn), chromium (Cr), cadmium (Cd) and lead (Pb) content of benthic fauna in the southeast coast of the Caspian Sea, where the major fish restocking programs are conducted. Seasonal sampling was performed in three sampling sites: north Miankaleh (NM), south Miankaleh (SM) and Gharesoo coast (GC). Results showed that sampling sites, sampling seasons and sampling sites × sampling seasons interaction had a significant effect on the heavy metal levels (p < 0.05). The yearly heavy metal concentration order was as follows: Zn > Pb > Cd > Cr. Yearly Pb levels of the NM site were significantly higher than the other sites. Also, yearly Cr levels of the SM site were significantly higher than site GC. Comparison of the benthos heavy metal levels with the available reference values suggests that the benthos tissues might be highly polluted which can intoxicate the fish feeding on them.