The adsorption mechanism of ammonium (NH4+) ion onto graphene quantum dots (GQDs) surface, modified with vacancy and heteroatom (nitrogen (N) and oxygen (O)), has been studied using a combination of dispersion-corrected density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) approaches in aqueous media. The potential of GQD-NX and GQD-OX surfaces as highly effective adsorbents for NH4+ ions has been explored by detailed analysis of adsorption energies, molecular electrostatic potential, charge transfer, density-of-states, non-covalent interaction, and desorption time. It has been observed that the adsorption of NH4+ ions on the GQD-NX surfaces is primarily chemisorption, governed by electrostatic interactions and hydrogen bonds. However, adsorption of NH4+ over the surface of GQD-OX predominantly ranges from strong physisorption to weak chemisorption arising from van der Waals interactions and hydrogen bonds. These findings present compelling new approach utilizing modified GQDs as highly efficient adsorbents for removing NH4+ ions from water.