The aggregation kinetics of two types of ZnO nanoparticles were investigated under various conditions. Distinct differences in aggregation kinetics were observed between the two ZnO particles. The aggregation of the nearly spherical ZnO (denoted as Me ZnO) exhibited strong dependence on the ionic strength (IS) of the solution; while minimal influence of IS was seen on the irregularly shaped ZnO (mixture of slab-like and rod-shaped particles, denoted as Mk ZnO) in the IS ranged tested. It is postulated that Mk ZnO possesses a critical coagulation concentration (CCC) below the lowest electrolyte concentration tested (1 mM NaCl) due to the interactions between various surfaces. The CCC of ZnO was found to be a function of pH; the CCC increased significantly as the pH was further away from the point of zero charge. Natural organic matter (NOM) was found to substantially hinder the aggregation of both types of ZnO particles (above 10 mg/L for Me ZnO and above 1 mg/L for Mk ZnO). A Langmuir adsorption model was used to describe the NOM to ZnO nanoparticle adsorption isotherms. To our knowledge, this is the first study to report the effect of particle morphology on nanoparticle aggregation, which outlines the importance of accounting morphology into environmental transport assessment of nanoparticles.