Natural iron oxides nanomaterials have important roles in biogeochemical processes. In this study, the effects of pH, natural organic matter, and cations on aggregation and sedimentation of natural goethite and artificial Fe3O4 nanoparticles in water were investigated to learn more about the environmental behaviors of engineered and natural nanomaterials and how they differ. In addition, a novel extended DLVO theory that considered steric, gravitational, and magnetic attraction forces concurrently was specifically developed to provide mechanisms explanations. Specifically, Fe3O4 NPs were more likely than bulk goethite to aggregate (because of magnetic attraction interactions) at low HA concentrations and disperse at high HA concentrations. Besides, goethite was less prone to settle with the same concentration of NaCl than Fe3O4 NPs, but the opposite trend was found for the same concentration of CaCl2 because of the difference in maximum net energy (barrier) and strong Ca2+ bridging effectiveness of goethite in CaCl2 solution. Statistical models were established to evaluate colloidal stability of the particles. XPS and molecular dynamics simulation results suggested that ions were adsorbed onto particles via ionic polarization and that the binding free energies at high coverage followed the order Ca2+ > Na+ > Cl- and presence of cation bridging between particles.