In this paper the adsorption activity of perlite nanoparticles for removal of Cu2+, Fe2+ and Mn2+ ions at Iran Sarcheshmeh copper acid mine drainage was discussed. Thus, raw perlite that provided from internal resource was modified and prepared via particles size reduction to nano scale and characterized by X-ray diffraction, X-ray fluorescence, scanning electron microscopy, transmission electron microscopy, Fourier transforms infrared and BET specific surface area analysis. The results of acid mine drainage show that pH of acid mine drainage is 5.1 and Cu2+, Fe2+ and Mn2+ ions are 10.5, 4.1 and 8.3 ppm, respectively. Firstly in the batch system the influence of adsorbent dose and temperature parameters were considered and then isothermal and kinetic models were investigated. According to the results the Langmuir isotherm and pseudo-second order kinetic model showed better correlation with the experimental data than other isotherm and kinetic models. Obtained thermodynamic parameters such as ΔG°, ΔH° and ΔS° show that the Cu2+, Fe2+ and Mn2+ ions adsorption from acid mine drainage is spontaneous and endothermic. Finally, perlite nanoparticles adsorbent was packed inside a glass column and used for the removal of heavy metals in 1, 3, 5 ml/min acid mine drainage flow rates, the breakthrough curves show that the column was saturated at 180, 240 and 315 min for different flow rates, respectively. According to the obtained results, this abundant, locally available and cheap silicate mineral showed a great efficiency for the removal of heavy metal pollutants from acid mine drainage and can be utilized for much volume of acid mine drainage or industrial scale.