Comprehensive experimental quantification and mapping of the aggregation and dispersion state of engineered nanoparticles (NPs) in the presence of humic substances is a great challenge. Dissipative particle dynamic (DPD) simulation was adopted to investigate the aggregation and dispersion mechanisms of NPs in the presence of a humic substance analog. Twelve different types of NPs including 2 metal-based NPs, 7 metal oxide-based NPs, and 3 carbon-based NPs in pure water (pH 3.0) and algae medium (pH 8.0) in the presence of a humic substance analogy were selected for experimental verification of the DPD simulation results. In agreement with results obtained with dynamic light scattering and phase analysis light scattering techniques, the simulations demonstrated that the presence of humic substances reduced the aggregation extent of the NPs. The DPD simulations showed that the stability and dispersity of the NPs increased first, and then decreased with increasing concentrations of humic substances. Moreover, there existed a concentration of humic substances where the NPs became more stable and more dispersed, which was experimentally verified in the case of all the NPs in the pure water and in the algae medium. Furthermore, theory and simulation indicate that both hydrophobic and hydrogen interaction play an important role in controlling the formation of NP aggregates in the presence of humic substances. Electrostatic interaction and steric repulsion are the main mechanisms underlying the effects of humic substances on the aqueous dispersion stability of NPs. Environ Toxicol Chem 2018;37:1024-1031. © 2017 SETAC.