The surface sediments of Seybouse River and its affluents have been studied and assessed to determine their degree of heavy metal contamination (Cd, Pb, Cu, Ni, Zn and Fe). The contamination factor (CF), the contamination degree (CD) and statistical tools (correlation and APC) has been used in assessing: metal contamination, sediment toxicity and to identify the origin of metals which have enriched the sediments. Heavy metals concentrations of sediments are generally heterogeneous and vary according to the metal and the sampling site. The results have been compared to the reference values of the unpolluted sediments and have shown that Seybouse River sediments are more contaminated by Pb, Cd and Zn respectively. CF values indicate moderate to considerable contamination for most stations. CD values show that the most toxic sediments are located mainly at the estuary and downstream of large agglomerations. The matrix correlation between the metallic elements shows a very strong correlation between Pb, Cd, Cu and Zn indicating that they have a similar source. These different metallic elements appear as traces of anthropogenic pollution. Despite using wastewater treatment plants as protective measures, Seybouse River pollution is remaining a big issue and more efforts has to be done by local authorities.