Manufactured nanoparticles (MNPs) are increasingly released into the environment and thus research on their fate and behaviour in complex environmental samples is urgently needed. The fate of MNPs in the aquatic environment will mainly depend on the physico-chemical characteristics of the medium. The presence and concentration of natural organic matter (NOM) will play a significant role on the stability of MNPs by either decreasing or exacerbating the aggregation phenomenon. In this study, we firstly investigated the effect of NOM concentration on the aggregation behaviour of manufactured Fe-oxide nanoparticles. Then, the stability of the coated nanoparticles was assessed under relevant environmental conditions. Flow field-flow fractionation, an emerging method which is gaining popularity in the field of nanotechnology, has been employed and results have been compared to another size-measurement technique to provide increased confidence in the outcomes. Results showed enhanced stability when the nanoparticles are coated with NOM, which was due to electrosteric stabilisation. However, the presence of divalent cations, even at low concentration (i.e. less than 1 mM) was found to induce aggregation of NOM-coated nanoparticles via bridging mechanisms between NOM and Ca2+.