Magnetic nanoparticles have gained significant attention as versatile adsorbents in various studies due to their easy application, simple synthesis, cost-effectiveness, and reusability. In this study, we synthesized magnetic poly(AMA-co-GMA) nanoparticles (MAG) and modified them using allyl methacrylate (AMA) and glycidyl methacrylate (GMA). The epoxy groups on the nanoparticles were opened to introduce –OH, –NH2, and –SH functional groups. The structural properties of the synthesized nanoparticles were characterized by FTIR, their morphology by SEM–EDS, TEM, BET, and XRD, their magnetic properties by VSM, and the thermal properties by the TGA analysis. MAG and the modified nanoparticles (MAG-OH, MAG-NH2, and MAG-SH) were then employed in batch adsorption experiments for heavy metal ions, including Cd2+, Cu2+, Zn2+, Ni2+, Pb2+, and Hg2+. The effect of pH, contact time, ion concentration, and temperature on adsorption was investigated, and kinetic, isotherm, and thermodynamic parameters were determined. Pb2+ and Hg2+ exhibited higher adsorption capacities among the tested heavy metal ions, prompting further investigation with MAG and MAG-SH nanoparticles. The experimental data suggested that the adsorption followed the second order kinetic and Langmuir isotherm models. Overall, the results highlight the excellent potential of the synthesized magnetic nanoparticles for effectively removing heavy metal ions from wastewater.