The stability and bioavailability of nanoparticles is governed by the interfacial properties that nanoparticles acquire when immersed in a particular aquatic media as well as the type of organism or cell under consideration. Herein, high-throughput screening (HTS) was used to elucidate ZnO nanoparticle stability, bioavailability, and antibacterial mechanisms as a function of iron doping level (in the ZnO nanoparticles), aquatic chemistry, and bacterial cell type. ζ-Potential and aggregation state of dispersed ZnO nanoparticles was strongly influenced by iron doping in addition to electrolyte composition and dissolved organic matter; however, bacterial inactivation by ZnO nanoparticles was most significantly influenced by Zn(2+) ions dissolution, cell type, and organic matter. Nanoparticle IC(50) values determined for Bacillus subtilis and Escherichia coli were on the order of 0.3-0.5 and 15-43 mg/L (as Zn(2+)), while the IC(50) for Zn(2+) tolerant Pseudomonas putida was always >500 mg/L. Tannic acid decreased toxicity of ZnO nanoparticles more than humic, fulvic, and alginic acid, because it complexed the most free Zn(2+) ions, thereby reducing their bioavailability. These results underscore the complexities and challenges regulators face in assessing potential environmental impacts of nanotechnology; however, the high-throughput and combinatorial methods employed promise to rapidly expand the knowledge base needed to develop an appropriate risk assessment framework.