<p>One of the primary causes of water contamination is heavy metal ions, some of which have been found to have carcinogenic characteristics. Such contamination poses a serious threat to aquatic ecosystems and represents a significant risk to human health. Due to its great sensitivity and efficacy, electrochemical detection is beneficial in light of the growing need for heavy metal detection. Schiff base functionalised magnetic nanoparticles Fe₃O₄/SiO₂/SB were synthesized and applied for the detection of heavy metal ions in water, including Pb²⁺, Hg²⁺ and Cd²⁺. Fe₃O₄/SiO₂/SB formation was verified by FT-IR, FESEM, TEM, EDS, TGA, XPS, BET and VSM. Square wave anodic stripping voltammetry (SWASV) was used to determine the analyte cations. The effects of experimental variables on the performance of the modified magnetic electrode were investigated and optimised. The sensor was effectively used to detect Pb²⁺, Hg²⁺ and Cd²⁺ in the presence of various potentially interfering ions. The detection limits were found to be 0.09&#xa0;µg L^− 1 for Pb²⁺, 0.014&#xa0;µg L^− 1 for Hg²⁺ and 0.08&#xa0;µg L^− 1 for Cd²⁺ with sensitivities of 1.42, 3.12 and 1.50 µA/µgL^− 1 respectively, when the electrochemical sensor was employed to determine the presence of heavy metal ions in water samples. DFT calculation showed that the detection of Pb²⁺, Hg²⁺ and Cd²⁺ is dominated by the interaction between the N atom and the metal ion. During complexation, charge is transferred from the Schiff base ligand to Pb²⁺, Hg²⁺ and Cd²⁺. Under the optimized SWASV conditions, the Fe₃O₄/SiO₂/SB sensor exhibits a linear response for all three ions in the range 0.2–20 µgL^− 1 and gives recoveries of 96.8–99.6% in spiked tap and river water samples.</p> Graphical abstract <p></p>