Environmental transformation through sulfidation and complexation with natural organic matter (NOM) are two major factors that may affect the fate and transport of silver nanoparticles (AgNPs) in the aquatic systems by changing their dissolution, deposition, and surface properties. To understand the impact of sulfidation and NOM on the aggregation and deposition of AgNPs, a combination of dynamic light scattering and quartz crystal microgravimetry with dissipation monitoring was used. Polyvinylpyrrolidone (PVP)-capped AgNPs that were modified through sulfidation and/or complexed with NOM had a greater extent of deposition than unmodified PVP-AgNPs. Specifically, the deposition extent of sulfidized AgNPs in the presence of NOM, which was the most environmental-relevant form in this study, was 0.5 to almost 3 orders of magnitude greater than unmodified PVP-AgNPs. Bare-silica and NOM-coated substrates were used as a basis for differentiating the effect of substrate on the deposition of PVP-capped AgNPs. Bare-silica substrate was more favorable for the deposition of modified PVP-capped AgNPs (including sulfidized, NOM-complexed, and sulfidized in the presence of NOM) than NOMcoated substrates. Citrate-capped AgNPs were also investigated to study the effect of capping agents on the deposition and surface properties of AgNPs. Since deposition extent implicates the degree of susceptibility to removal by water treatment, citrate-capped AgNPs, which have 6 to 50 orders of magnitude less deposition than PVP-capped AgNPs, are more likely to persist in the aquatic environments.