The present study investigated how humic substances (HS) modify the aquatic toxicity of silver nanoparticles (AgNPs) as these particles agglomerate in water and interact with HS. An alga species (Raphidocelis subcapitata), a cladoceran species (Chydorus sphaericus), and a freshwater fish larva (Danio rerio), representing organisms of different trophic levels, were exposed to colloids of the polyvinylpyrrolidone-coated AgNPs in the presence and absence of HS. Results show that the presence of HS alleviated the aquatic toxicity of the AgNP colloids to all the organisms in a dose-dependent manner. The particle size distribution of the AgNPs' colloidal particles shifted to lower values due to the presence of HS, implying that the decrease in the toxicity of the AgNP colloids cannot be explained by the variation of agglomeration size. The surface charge of the AgNPs was found to be more negative in the presence of high concentrations of HS, suggesting an electrostatic barrier by which HS might limit interactions between particles and algae cells; indeed, this effect reduced the algae toxicity. Observations on silver ions (Ag(+)) release show that HS inhibit AgNP dissolution, depending on the concentrations of HS. When toxic effects were expressed as a function of each Ag-species, toxicity of the free Ag(+) was found to be much higher than that of the agglomerated particles.