The aim of this work is to evaluate the influence of a spatial salinity gradient, as encountered in an estuarine when fresh water meets salty one, on the aggregation features of fullerene nanoparticles aggregates (nC60). To model these environmental conditions, we design a specific microfluidic device. In literature, physical phenomena occurring in estuarine area, such as the salinity gradient and the flow conditions, were never considered. Our results suggest that even a short time exposure (couple of seconds) to a salinity gradient, i.e. dynamical spatial conditions, profoundly affects the aggregation properties of nanoparticles and therefore their environmental behavior and fate. It appears that a salinity gradient could enhanced the stability of nanoparticles, especially at high ionic strength (closed to the seawater level one). Contrary to the common approach of particle aggregation in the lab in environmental conditions, our study shows the need to reconsider the spatial and temporal variation of abiotic parameters (ionic strength, pH, organic matter concentration) in the understanding and the evaluation of nanoparticles environmental fate and transportation mechanisms.