A novel hybrid nanomaterial, nanoscale zero-valent iron (nZVI)-grafted imogolite nanotubes (Imo), was synthesized via a fast and straightforward chemical procedure. The as-obtained nanomaterial (Imo-nZVI) was characterized using transmission electron microscopy (TEM), electrophoretic mobility (EM) and vibrating sample magnetometry (VSM). The prepared Imo-nZVI was superparamagnetic at room temperature and could be easily separated by an external magnetic field. Sorption batch experiments were performed in single- and multicomponent system and showed that Hg2+ and Pb2+ could be quantitatively adsorbed at pH 4.0 with maximum adsorption capacities of 62.3 and 73.8 mg·g− 1, respectively. It was observed that the functional groups in Imo-nZVI interact preferentially with analytes according to Misono Softness parameter. The higher performance of Imo-nZVI compared with Imo and nZVI is related to the increased adsorption sites in the functionalized nanomaterial. The sorption equilibrium data obeyed the Langmuir model, while kinetic studies demonstrated that the sorption processes of Hg2+ and Pb2+ followed the pseudo-second-order model. This study suggests that the Imo-nZVI composite can be used as a promising sorbent and provides a simple and fast separation method for the removal of Hg and Pb ions from contaminated water.