In this work, indium tin oxide (ITO) electrodes were functionalized with varying 3-aminopropyltriethoxysilane (APTES) concentration percentages (0.5, 0.75, 1.0, and 2.0 wt %) to obtain the optimum conditions for the assembly of the as-synthesized gold nanoparticles (AuNPs). The AuNP coverage, wettability, and electrochemical performance of the modified electrodes were evaluated. The AuNP/0.75% APTES-ITO-modified electrode exhibited uniform coverage of AuNPs and high electrochemical performance for the simultaneous detection of Cd(II), Pb(II), and Cu(II) ions. Under the optimum conditions, the AuNP/0.75% APTES-ITO-modified electrode showed a linear detection range of 5–120 ppb and limit of detection of 0.73, 0.90, and 0.49 ppb for the simultaneous detection of Cd(II), Pb(II), and Cu(II) ions, respectively, via square wave anodic stripping voltammetry. The modified electrode demonstrated good anti-interference toward other heavy metal ions, good reproducibility, and suitability for application in environmental sample analysis.