Aggregation of nanoparticles impacts their reactivity, stability, transport, and fate in aqueous environments, but limited methods are available to characterize structural features and movement of aggregates in liquid. Here, liquid cell transmission electron microscopy (LCTEM) was utilized to directly observe the size, morphology, and motion of aggregates that were composed of 9 and 36 nm hematite nanoparticles, respectively, in water or NaCl solution. When mass concentrations were same, the aggregates of 9 nm nanoparticles were statistically more compact and slightly larger than those of 36 nm nanoparticles. Aggregates in both samples were typically nonspherical. Increasing ionic strength resulted in larger aggregates, and also enhanced the stability of aggregates under electron-beam irradiation. In water, small aggregates moved randomly and approached repeatedly to large aggregates before final attachment. In NaCl solution, small aggregates moved directly toward large aggregates and attached to the latter quickly. This observation provided a direct confirmation of the DLVO theory that the energy barrier to aggregation is higher in water than in salt solutions. This study not only presented the influences of particle size and ionic strength on aggregation state, but also demonstrated that LCTEM is a promising method to link aggregation state to dynamic processes of nanoparticles.