Herein, we report the first example of a supramolecular carbon nanotube (CNT)-based magnetic depolluting agent for divalent metal ion (M2+) removal from aqueous solutions. In particular, magnetic multi-walled carbon nanotubes (m-MWCNTs) coated with poly(vinylpyridine) (PVPy) self-aggregate in aqueous solutions that contain divalent metal ions (such as Zn2+, Cu2+ and Pb2+) to form tight insoluble bundles in which the M2+ ions remain trapped through pyridyl–M2+–pyridyl interactions. Magnetic filtration ultimately affords the efficient separation of the depolluted solution from the precipitated M2+-CNT agglomerates. Upon acid treatment, the supramolecular threads could be disassembled to afford the free CNT–polymer hybrid, thus allowing recycling of the depolluting agent. All materials and complexation/decomplexation steps were thoroughly characterised by using thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS), transmission and scanning electron microscopy (TEM and SEM, respectively). The quantification of the M2+ residual concentrations in water was evaluated by using inductively coupled plasma optical emission spectroscopy (ICP-OES), which showed that, depending on the metal cation, this material can remove up to 99 % of the contaminant.