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Monitoring water quality has become a goal to prevent issues related to human health and environmental conditions. In this sense, the concentration of metal ions in water sources is screened, as these are considered persistent contaminants. In this work, we describe the implementation of customized graphite electrodes decorated with two types of Hg nanoparticles (Hg-NPs), optimized toward the electrochemical detection of Cd, Pb and Cu. Here, we combine Hg, a well-known property to form alloys with other metals, with the nanoscale features of Hg-NPs, resulting in improved electrochemical sensors towards these analytes with a substantial reduction in the used Hg amount. Hg-NPs were synthesized using poly(diallyldimethylammonium) chloride (PDDA) in a combined role as a reducing and stabilizing agent, and then appropriately characterized by means of Transmission Electron Microscopy (TEM) and Zeta Potential. The surface of composite electrodes with optimized graphite content was modified by the drop-casting of the prepared Hg-NPs. The obtained nanocomposite electrodes were morphologically characterized by Scanning Electron Microscopy (SEM), and electrochemically by Cyclic Voltammetry (CV) and Electrochemical Impedance Spectroscopy (EIS). The results show that the Hg-NP-modified electrodes present better responses towards Cd(II), Pb(II) and Cu(II) detection in comparison with the bare graphite electrode. Analytical performance of sensors was evaluated by square-wave anodic stripping voltammetry (SWASV), obtaining a linear range of 0.005–0.5 mg·L−1 for Cd2+, of 0.028–0.37 mg·L−1 for Pb2+ and of 0.057–1.1 mg·L−1 for Cu2+. Real samples were analyzed using SWASV, showing good agreement with the recovery values of inductively coupled plasma–mass spectrometry (ICP-MS) measurements.