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In order to investigate the behavior, distribution, and characteristics of heavy metals including rare earth elements (REEs), thorium (Th), and uranium (U) in sludge, the total and fractional concentrations of these elements in sludge collected from an industry water treatment plant were determined and compared with those in natural soil. In addition, the removal/recovery process of heavy metals (Pb, Cr, and Ni) from the polluted sludge was studied with biosurfactant (saponin and sophorolipid) elution by batch and column experiments to evaluate the efficiency of biosurfactant for the removal of heavy metals. Consequently, the following matters have been largely clarified. (1) Heavy metallic elements in sludge have generally larger concentrations and exist as more unstable fraction than those in natural soil. (2) Nonionic saponin including carboxyl group is more efficient than sophorolipid for the removal of heavy metals in polluted sludge. Saponin has selectivity for the mobilization of heavy metals and mainly reacts with heavy metals in F3 (the fraction bound to carbonates) and F5 (the fraction bound to Fe-Mn oxides). (3) The recovery efficiency of heavy metals (Pb, Ni, and Cr) reached about 90–100% using a precipitation method with alkaline solution.