The application of nanoparticles in the processes of making commercial products has increased in recent years due to their unique physical and chemical properties. With increasing amount of commercial nanoparticles released into nature, their fate and effects on the ecosystem and human health are of growing concern. This study investigated the stability and morphology of three metal oxide nanoparticles in aqueous solutions. The commercially available nanoparticles, TiO2, ZnO, SiO2, aggregated quickly into micrometer-size particles in aqueous solutions, which may not threaten human health. Their changes in morphology and characteristics were further examined by dynamic light scattering (DLS) method and transmission electron microscopy (TEM). Among the several dispersion approaches, ultrasonication was found to be the most effective for disaggregating nanoparticles in water. For these three selected nanoparticles, ZnO could not remain stable in suspensions, presumably due to the dissolution of particles to form high concentration of ions, resulting in enhanced aggregation of particles. In addition, the existence of dissolved organic matters stabilized nanoparticles in lake water and wastewater for several hours in spite of the high concentration of cations in these real-water samples. The fate of metal oxide nanoparticles in natural water bodies would be determined by the type and concentration of cations and organic matters. Results obtained in this study revealed that the stability of nanoparticles changed under different aqueous conditions and so did their fate in the environment.