This study is the first report of its type demonstrating the synthesis of mHAP on the basis of magnetic functionalization with nHAP, which were synthesized using Rutilus frisii kutum fish scale as a benign fishery waste by-product. The mHAP was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray diffraction (EDX), and Fourier transform infrared (FT-IR) spectroscopic techniques. The XRD pattern confirmed the formation of a single-phase nHAP without any extra steady phases. It was also found that the pseudo-second-order kinetic model gave a satisfactory fit to the experimental data (R2 = 0.99). The maximum removal percentages of Cu and Zn ions in optimal conditions (adsorbent dosage at 0.1 g, 30 min contact time at 25 ± 1 °C and pH = 5 ± 0.1) by mHAP were 97.1% and 93.8%, respectively. Results also demonstrated that mHAP could be recycled for up to five cycles in the case of copper and zinc. The Langmuir isotherm was proved to have a better correlation compared with that of the Freundlich isotherm. The thermodynamic parameters indicated that it was a spontaneously endothermic reaction. In conclusion, mHAP could be regarded as a powerful candidate for efficient biosorbent, capable of adsorbing heavy metals from aqueous solutions.