Available information about the application of clay minerals (e.g. sepiolite) at nanoscale levels for stabilization of potentially toxic trace elements in soils and wastewaters is very limited. Therefore, this study was carried out to: (i) determine how removal of Pb and Cu from aqueous solutions (containing 150 mg/kg Pb and Cu) differs between microparticles (<10 μm) and nanoparticles (<100 nm) of sepiolite, and (ii) find out the kinetic parameters of Pb and Cu adsorption onto micro- and nano-sized particles of sepiolite. Batch experiments at eleven contact times (5, 10, 20, 30, 60, 120, 240, 480, 720, 1440 and 2880 min) with three replications were conducted and the data were evaluated using pseudo-first order, pseudo-second order, and intraparticle diffusion models. The results indicated that the sorption of Pb and Cu onto both microparticles and nanoparticles of sepiolite follows an increasing trend with contact time, and it is a three-stage process that is well described by the pseudo-second-order kinetic model. Intraparticle diffusion modeling showed that intraparticle diffusion was not the only mechanism that influenced the rate of Pb and Cu uptake by the nano- and microparticles of sepiolite. The maximum adsorptions of Pb and Cu by sepiolite nanoparticles were 34.70 and 24.50 mg g−1, respectively, higher than those of the microparticles (27.17 and 17.10 mg g−1). To identify how the addition of sepiolite nanoparticles (10 and 20 g/kg soil) would function as a soil amendment relative to Pb and Cu pollution, the leaching potential of Pb and Cu was also tested, using distilled water and 1 M NH4NO3 solutions from the two soils with clay loam and sandy loam textures. The results implied that the addition of sepiolite nanoparticles to both the sandy loam and clay loam soils increased their ability to retain Pb and Cu elements in comparison with the control. In both the clay loam and sandy loam soils, the amounts of Pb and Cu leached using the 1 M NH4NO3 solution were significantly higher than those with distilled water. The amounts of metals eluted using 1 M NH4NO3 solution from the sandy loam and clay loam soils treated with 20 g kg−1 nanoparticles of sepiolite were 7.15% and 5.33% for Cu, and 6.44% and 4.55% for Pb, respectively. The results also illustrated that using water and NH4NO3 solutions, the metal extraction yield was greater in the sandy loam soil than in the clay loam soil. The highest amounts of Pb (9.76%) and Cu (9.88%) leached from the soils were observed in the sandy loam soil, using 1 M NH4NO3 solution, but without any addition of sepiolite nanoparticles. In contrast, the clay loam soil leached with water and amended with 20 gkg−1 sepiolite nanoparticles showed the least amount of Pb (3.49%) and Cu (3.93%) in the leachates. In conclusion, sepiolite nanoparticles improved the efficiency of Pb and Cu removal from aqueous solutions and their immobilization in soils with sandy loam and clay loam textures. The findings also emphasize the importance of extracting agents in evaluating the amounts of Pb and Cu leached from the soils.