A simple, fast, and economic methodology to fabricate a highly efficient superparamagnetic Fe3O4/hydroxyapatite nanocomposite (MHAP) was successfully developed. Hydroxyapatite was functionalized with magnetite nanoparticles through coprecipitation-assisted microwave processes to improve the magnetic properties. The synthesized magnetic hybrid adsorbent matrix was investigated by different methods. Transmission electron microscopy demonstrated a good impregnation of Fe3O4 on the hydroxyapatite matrix with uniform morphology. Magnetic hysteresis measurement revealed that MHAP nanocomposites exhibit excellent strong, soft-magnetic properties. The synergistic effect was an evidence for iron and manganese ion removal, enlightening their potentialities in treatment of polluted ground water.