Understanding the colloidal stability of functionalized engineered nanoparticles (FENPs) in aquatic environments is of paramount importance in order to assess the risk related to FENPs. In this study, gold nanoparticles (GNPs) of 68 and 43 nm diameter, coated with citrate and 11-mercaptoundecanoic acid (MUA) respectively, were used as models of FENPs. Time-resolved dynamic light scattering was employed to investigate the aggregation kinetics of two types of GNPs. The results show that without Suwannee river natural organic matter (SRNOM), MUA coating resulted in greater stability than citrate coating for GNPs. Cations have a destabilizing effect on both GNPs following the order Ca(2+) ≈ Mg(2+) >> Na(+); different anions (Cl(-) and SO4(2-)) showed no difference in effects. In the fast aggregation regime, adding SRNOM enhanced the stability of MUA-coated GNPs in both Ca(2+) and Mg(2+) solutions. However citrate-coated GNPs were only stabilized in Mg(2+) solution but enhanced aggregation occurred in high Ca(2+) concentration due to interparticle bridging. For the investigated GNPs and in the presence of SRNOM, Ca(2+) does not always act as a strong coagulant. This indicates that for the new materials emerging from the application of nanotechnology the well-described aggregation mechanisms of colloids in the environment require a detailed re-examination.