Understanding the transformation and transport of manufactured nanoparticles (NPs) in aquatic systems remains an important issue due to their potential hazard. Once released in aquatic systems, NPs will interact with natural compounds such as suspended inorganic particles and/or natural organic matter (NOM) and heteroaggregation will control their ultimate fate. Unfortunately, systematic experimental methods to study heteroaggregation are not straightforward and still scarce. In addition, the description of heteroaggregation rate constants and attachment efficiencies is still a matter of debate since no clear definition exists. In this work, an original cluster-cluster Monte Carlo model is developed to get an insight into heteroaggregation process descriptions. A two-component system composed of NPs and NOM fulvic acid monomers is investigated by considering several water models to cover a range of (relevant) conditions from fresh to marine waters. For that purpose, homo- and hetero- individual attachment efficiencies between NPs and NOM units are adjusted (NP-NP, NOM-NOM and NP-NOM). The influence of NP/NOM ratio, NOM-NOM homoaggregation versus heteroaggregation, and surface coating effects is studied systematically. From a quantitative point of view, aggregation rate constants as well as attachment efficiencies are calculated as a function of physical time so as to characterize the individual influence of each parameter and to allow future comparison with experimental data. Heteroaggregation processes and global attachment efficiencies corresponding to several mechanisms and depending on the evolution of heteroaggregate structures all along the simulations are defined. The calculation of attachment efficiency values is found dependent on NP/NOM concentration ratios via coating effects, by the initial set of elementary attachment efficiencies and influence of homoaggregation. Marine water represents a specific case of aggregation where all particle contacts are effective. On the other hand, in “ultrapure” and “fresh waters”, a competition between homo- and heteroaggregation occurs depending on the initial attachment efficiencies therefore indicating that a subtle change in the NP surface properties as well as in the water chemistry have a significant impact on heteroaggregation processes