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In this study, the biosurfactant-enhanced electrokinetic method was investigated for the removal of potentially toxic trace elements (As, Ba, Cd, Cr, Cu, Mo, Ni, Pb, Sb, Se and Zn) in waterways sediments. The effect of this method was compared to the removal capacities of deionized water in the same conditions in order to assess its efficiency. After treatment, batch leaching tests have shown that almost toxic elements (As: 81.3%; Ba: 80%; Cr: 97.3%; Cu: 82%; Zn: 94.5%; Mo: 13.8%; Ni: 62.7%; Se: 66.8% and Sb: 9.3%) were less released in waters. On the whole sediment samples, Ba and Cd displayed the highest removal rates (Ba: 71.2% and Cd: 77.5%). The use of biosurfactant enhanced the electrokinetic method by improving the trace elements migration and altering pH and Eh locally generated by the system. Overall, the application of this new approach dredged sediments seems to be promising but needed further investigations for industrial applications.