The present work describes the successful functionalization/magnetization of bio-polymeric spores of Lycopodium clavatum (sporopollenin) with 1-(2-hydroxyethyl) piperazine. Analytical techniques, i.e., Fourier transform infrared (FT-IR), field emission scanning electron microscope (FESEM), energy-dispersive X-ray spectroscopy (EDS), and vibrating sample magnetometer (VSM), were used to confirm the formation of 1-(2-hydroxyethyl) piperazine-functionalized magnetic sporopollenin (MNPs-Sp-HEP). The proposed adsorbent (MNPs-Sp-HEP) was used for the removal of noxious Pb(II) and As(III) metal ions from aqueous media through a batch-wise method. Different experimental parameters were optimized for the effective removal of selected noxious metal ions. Maximum adsorption capacity (q ) 13.36 and 69.85 mg g for Pb(II) and As(III), respectively, were obtained. Thermodynamic parameters such as free energy (ΔG°), entropy (ΔS°), and enthalpy (ΔH°) were also studied from the adsorption results and were used to elaborate the mechanism of their confiscation. The obtained results indicated that newly adsorbent can be successfully applied for the decontamination of noxious Pb(II) and As(III) from the aqueous environment.