Achieving affordable and clean water is one of the greatest global challenges of this century. This is due to the enormous upsurge in the world's population, yet at the same time, the scarcity of fresh water. Far more than that, some regions are awash in fresh water while other regions are afflicted by drought. Accordingly, new technological approaches should be brought to the forefront to tackle the water problem. Hence, this study presents three types of newly in-house prepared silica-embedded NiO and/or MgO nanoparticles, namely; SiO2–NiO, SiO2–MgO, and SiO2–(Ni0.5Mg0.5)O. The properties of these nanoparticles were characterized using XRD, BET, HRTEM, CO2-TPD, and IR spectroscopy. These nanoparticles are applied for the first time to adsorptive removal of different cationic and anionic model organic molecules with different functionalities, namely: methylene blue (MB), neutral red (NR), and acid red 27 (AR27), mimicking pollutants existing in wastewater effluents. It has been found that on a normalized surface area basis, the number of cationic model molecules adsorbed per nm2 of the SiO2–(Ni0.5Mg0.5)O nanoparticles were the highest suggesting the possible synergistic effect between Ni and Mg in the mixed oxide, however, SiO2–NiO showed the highest uptake for the anionic case due to its stability in aqueous solutions. The experimental adsorption isotherms fit well to the Sips model for MB and AR27 indicating a heterogeneous adsorption system. However, a multilayer adsorption behavior was obtained for NR which has been described by the BET model. Computational modeling and DFT calculations of the interaction between the model molecules and the surfaces of the prepared nanoparticles were carried out to get more mechanistic insights into their adsorptive behaviors. The results showed that the adsorbed molecules tend to lie flat on the surface of the materials except for NR which tends to be adsorbed slightly tilted when compared with the others. Additionally, molecular dynamics simulation was performed to gain additional insights into the adsorption behavior of NR in the presence of water. The evolved profile of total energy of the system as a function of simulation time emphasized the eccentric BET adsorption behavior of NR onto these novel nanoparticles.