Adsorption of natural organic matter, aggregation and disaggregation have been identified as three of the main processes affecting the fate and behaviour of engineered nanoparticles (ENPs) in aquatic environments. However, although several methods have been developed to study the aggregation behaviour of ENPs in natural waters, there are only a few studies focusing on the fate of such aggregates and their potential disaggregation behaviour. In this study, we proposed and demonstrated a simple method for characterising the aggregation behaviour and aggregate structure of ENPs in different natural waters. Both the aggregate size of ENPs and their adsorption capacity for dissolved organic matter (DOM) were strongly related (R2 > 0.97, p < .05) to the combined effect of initial concentration of dissolved organic matter (DOM) and the ionic strength of the natural waters. The structure of the formed aggregates was strongly correlated (R2 > 0.95, p < .05) to the amount of DOM adsorbed by the ENPs during the aggregation process. Under high ionic strength conditions, aggregation is mainly governed by diffusion and the aggregates formed under these conditions showed the lowest stability and fractal dimension, forming linear, chain-like aggregates. In contrast, under low ionic strength conditions, the aggregate structure was more compact, most likely due to strong chemical binding with DOM and bridging mechanisms involving divalent cations formed during reaction-limited aggregation.