The widespread contamination of aqueous environments with micro and nanoplastics (MNPs) is an emergent environmental problem that has been gathering increasing public concern. In addition to the known harmful effects on the ecosystems and living organisms, there have been raising worries that MNPs may adsorb trace pollutants such as heavy metals and organics, accumulate them and substantially concentrate them relative to their concentrations in the original aqueous medium. The tendency of MNPs to adsorb compounds may be linked to the particle sizes as well as to their final shapes. In order to assess MNPs behavior in the water environment, namely in terms of particle shapes, structures, interactions and aggregation, differently sized nanoparticles of three common plastics, polyethylene, polyethylene terephthalate and the polyamide nylon 6, were analyzed by molecular dynamics simulations. In all cases, a fast and spontaneous aggregation of the initially dispersed nanoparticles was observed yielding one single larger nanoparticle. In spite of the differences in the type of interactions between each plastic and water, no dispersal and solubilization of any plastic chains was observed during the simulations. The form of aggregation of the various nanoclusters was however very different: compact and ordered for polyethylene, globular and stringy for nylon6, while the PET bent chains form entangled piled-up structures with the aromatic rings preferentially oriented in a parallel-wise ordered way. In addition to the observed aggregation of all the smaller nanoparticles, a rearrangement and a spontaneous self-assembling ordering of the chains was observed as well, particularly in the polyethylene case. The results reinforce the observed tendency of the plastic chains to remain stably associated in clusters with a significant size, in the form of nanoparticles that resist further fragmentation and degradation for all the types of plastic, although the shapes of the particles differ among plastic types.