The aggregation of nanoplastics (NPs) is a key issue in understanding the dynamic nature of NPs in the environment. The aggregation of NPs under various environmental conditions has not yet been studied. We investigated the influences of inorganic ions and natural organic matter (NOM) on polystyrene (PS) NPs aggregation in solutions. Results showed that PS NPs remained stable in wide ionic strength solutions of NaCl (1–100 mM) and CaCl2 (0.1–15 mM), and only in low ionic strength FeCl3 solutions (0.01 mM). However, obvious PS NPs aggregation was observed in FeCl3 solutions with an increase in ionic strength (0.1 and 1 mM). Moreover, NOM had a negligible effect on PS NPs aggregation in all ionic strengths of NaCl and CaCl2 solutions and in low ionic strength FeCl3 solutions (0.01 mM). However, NOM reduced PS NPs aggregation in an intermediate ionic strength FeCl3 (0.1 mM) solution and increased aggregation in a high ionic strength FeCl3 (1 mM) solution. Based on the theoretical analysis of interaction forces among PS NPs, the Derjaguin–Landau–Verwey–Overbeek force was a contributor governing PS NPs aggregation either in the absence or presence of NOM. In addition, other factors, including electrostatic heterogeneity of PS NPs surfaces, steric repulsion induced by NOM, and clusters formed via bridging effect in the presence of NOM also contributed to altered PS NPs aggregation under selected conditions. The PS NPs-NOM clusters were directly observed using a cryogenic scanning electron microscope.