Abstract The growing interest in nanoparticles (NP) is inevitably translating into an increase of their emissions in the environment. On the other hand, the necessary knowledge about the fate and transport of these NPs in the environment remains limited. In particular it is critically important to understand how the interactions of NPs with the particles already present in environmental matrices affect their fate, transport, and eventually persistence in the environment. In this study we present a computer model that expands upon the existing simple homogeneous aggregation models to account for heterogeneous aggregation between NPs and the distribution of natural particles already present in environmental waters. The model follows the concentrations of purely nanoparticle aggregates, purely background particles aggregates, and mixed aggregates, as well as the composition of mixed aggregates. After analytical evaluation, we ran simulations to illustrate the complexity of heterogeneous aggregation and its impact on the fate of NPs. The model predicts that the impact of NP size on their persistence in the environment is accentuated for low affinity between NPs and background particles, and for low background particle concentration.