Plastic debris are classified as a function of their size and recently a new class was proposed, the nanoplastics. Nano-sized plastics have a much greater surface area to volume ratio than larger particles, which increases their reactivity in aquatic environment, making them potentially more toxic. Only little information is available about their behavior whereas it crucially influences their toxicity. Here, we used dynamic light scattering (DLS) to explore the influence of environmental factors (fresh- and saltwater, dissolved organic matter) on the behavior (surface charge and aggregation state) of three different nano-polystyrene beads (50 nm), with (i) no surface functionalization (plain), (ii) a carboxylic or (iii) an amine functionalization. Overall, the positive amine particles were very mildly affected by changes in environmental factors with no effect of the salinity gradient (from 0 to 653 mM) and of a range 1–30 μg.L−1 and 1–10 μg.L−1 of organic matter in artificial seawater and ultrapure water, respectively. These observations are supposedly linked to a coating specificity leading to repulsive mechanisms. In contrast, the stability of the negatively charged carboxylic and plain nanobeads was lost under an increasing ionic strength, resulting in homo-aggregation (up to 10 μm). The increase in organic matter content had negligible effect on these two nanobeads. Analysis performed over several days demonstrated that nanoplastics formed evolving dynamic structures detected mainly with an increase of the homo-aggregation level. Thus, surface properties of given polymers/particles are expected to influence their fate in complex and dynamic aquatic environments.