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The functionalization of materials for ultrasensitive detection of heavy metal ions (HMIs) in the environment is crucial. Herewith, we have functionalized inexpensive and environmentally friendly Fe₃O₄ nanoparticles with D-valine (Fe₃O₄–D–Val) by a simple co-precipitation synthetic approach characterized by XRD, FE-SEM, and FTIR spectroscopy. The Fe₃O₄–D–Val sensor was used for the ultrasensitive detection of Cd⁺², Pb⁺², and Cu⁺² in water samples. This sensor shows a very low detection limit of 11.29, 4.59, and 20.07 nM for Cd⁺², Pb⁺², and Cu⁺², respectively. The detection limits are much lower than the values suggested by the world health Organization. The real water samples were also analyzed using the developed sensor.