Understanding how engineered nanoparticles (ENPs) interact with natural organic acids is important to ecological risk assessment of ENPs, but this interaction remains poorly studied. Here, we investigate the dispersion stability, ion release, and toxicity of yttrium oxide nanoparticles (nY2O3) suspensions after exposure to two low molecular weight natural organic acids (LOAs), namely benzoic acid and gallic acid. We find that in the presence of LOAs the nY2O3 suspensions become more stable with surface zeta potential more positive or negative, accompanied by small agglomerated size. LOA interaction with nY2O3 is shown to promote the release of dissolved yttrium from the nanoparticles, depending on the concentrations of LOAs. Toxic effects of the nY2O3 suspensions incubated with LOAs on Scenedesmus obliquus as a function of their mixture levels show three types of signs: stimulation, inhibition, and alleviation. The mechanism of the effects of LOAs on the nY2O3 toxicity may be mainly associated with the degree of agglomeration, particle-induced oxidative stress, and dissolved yttrium. Our results stressed the importance of LOA impacts on the fate and toxicity of ENPs in the aquatic environment.