The extensive use of engineered nanoparticles (ENPs) such as zinc oxide nanoparticles (ZnO NPs) in various commercial fields has spurred significant concern about its possible toxicological effects of ZnO NPs on human health and eco-system. Therefore, it is substantial to understand the aggregation phenomena which could attenuate this effect. This data article provides information on aggregation of ZnO NPs under the influence of various parameters of water chemistry. Moreover, Taguchi orthogonal array L27(313) design matrix was used to evaluate the effect of multiple parameters in aqueous solution. The data were obtained from single beam UV-Vis spectrophotometer (Optizen 2120 UV, Mecasys, Korea) using Optizenview 4.2.5 PC interference software, Fourier transform infrared spectrometer (FT/IR-4700, spectroscopy, JASCO Analytical Instruments, Easton, USA) and particle electrophoresis (NanoZS, Zetasizer, Malvern Instruments Ltd, Worcestershire, UK). The dataset draws attention on dominant parameters influencing aggregation of ZnO NPs in water. The analysis of variance (ANOVA) data revealed that electrolyte concentration, type and natural organic matter (NOM) concentration were the most significant parameters. Furthermore, FT-IR data presents a possible mechanism of ZnO NPs stabilization in the presence of different NOM. This data will be helpful for the development of environmental risk assessment strategies and prediction of fate and mobility of other ENPs in the aquatic environment.