A highly effective magnetic nanocomposite alginate beads (PPy-NTs/PEI@Alg@NiFe2O4) were synthesized using alginate as the encapsulation reagent and polypyrrole/polyethylene imine with nano NiFe2O4 as a functional filler to remove toxic Zn2+ and Pb2+ from polluted water. A response surface methodology (RSM) was used to statistically assess the influences of pH and the adsorbent dose on the adsorption performance. PPy-NTs/PEI@Alg@NiFe2O4 magnetic microbeads exhibited the optimal adsorption capacity qe (18.6 mg/g) at pH 6 and a 2 mg/L dose for Zn2+ removal. In comparison, the optimal qe (32.6 mg/g) was reached at pH 4.5 with a 1.5 mg/L dose for Pb2+ remediation. From batch experiments, maximal absorption capacities of 53.3 mg/g and 22 mg/g were achieved for Pb2+ and Zn2+, respectively, at 313 K. The pseudo-second-order kinetic model fitted the results well, suggesting that the chemisorption process regulates adsorption. Isotherm models indicate the presence of homogeneous adsorption sites from the well-fitting to Langmuir isotherm. An investigation of the effects of temperature and thermodynamic considerations revealed the endothermic nature of Zn2+ and Pb2+ absorption. The Fourier transform infrared spectra showed that –NH, –NH2, and –COO− are the main groups in PPy-NTs/PEI@Alg@NiFe2O4 composite beads that were responsible for Zn2+ and Pb2+ removal from polluted water.