In this work, a highly sensitive and selective colorimetric sensor assay for the detection of Hg2+ ions is presented utilizing an anti-aggregation sensing approach with AuNPs and an amine-based sensor (S). The addition of sensor (S) to gold nanoparticles (AuNPs) leads to their aggregation and, thus, color variation from red to blue. Whereas, in the presence of Hg2+ ions, i.e., target analyte, sensor (S) preferably binds with Hg2+ ions over AuNPs, thus inhibiting their aggregation and subsequent color change. This approach is optimized in terms of various analytical parameters, such as incubation time, pH effect, and S titration, to obtain high sensitivity and selectivity. The UV–Visible studies validate the performance of developed approach for Hg2+ ions detection, and the limit of detection was calculated to be 17 nM, which is lesser than its permissible limit (30 nM) in drinking water. The interference studies also confirm the develop approach selectivity for Hg2+ ions even in the presence of coexisting ions in aqueous media. The experimental results were further correlated with the computational density functional theory (DFT) studies. The presented method is not only cost-effective but also eliminates tedious synthetic schemes and need of laborious manpower.