In this study, the adsorptive removal of Zn2+, Cu2+, and Cr3+ metal ions from aqueous solutions onto NiO–MgO silica-based nanoparticles (SBNs) has been studied. The effect of several factors such as solution pH, initial concentration, contact time, and coexisting ions on the adsorbed amounts of single Zn2+, Cu2+, and Cr3+ ions have been investigated within an array of batch mode experiments. Interestingly, the adsorption of Cr3+ at high and low concentrations was very fast, and equilibrium was achieved within 2 min compared to Cu2+ and Zn2+ which needed 30 and 60 min to reach equilibrium, respectively. The adsorption equilibrium data fitted very well with the Sips adsorption isotherm model for Cu2+ and Zn2+, and the BET model for Cr3+ ions. The maximum uptake was maintained at 7.23, 13.76, 41.36 (ions per nm2) for Zn2+, Cu2+, and Cr3+, respectively. This equals to 37.69, 69.68, 209.51 (mg adsorbate per g adsorbent), respectively, showing the promising industrial application of those SBNs. Moreover, the adsorption uptake results increase with increasing the pH in the range of 7.0–11.0 for all investigated metal ions. The thermodynamic parameters such as the changes in Gibbs free energy (ΔGo), enthalpy (ΔHo), and entropy (ΔSo) were determined. The adsorption of Zn2+, Cu2+, and Cr3+ was spontaneous, endothermic, and physical for Cu2+ and Cr3+, while exothermic and chemical for Zn2+. The regeneration and reusability studies have proven that the NiO–MgO SBNs can be employed for the adsorptive of these metals repeatedly without impacting the adsorption capacity indicating their sustainability.