As engineered nanoparticles (NPs) are increasingly used, their entry into the environment has become an important topic for water sustainability. Recent investigations point to the critical role of natural organic matter (NOM) in altering the persistence of NPs by complexing with their surfaces. The NP-NOM complex, in turn, is the new entity that may potentially influence subsequent fate of NPs. To understand the relative impact of humic (HA) and fulvic fraction of NOM on the stability and mobility of silver nanoparticles (AgNPs), a combination of dynamic light scattering and quartz crystal microgravimetry with dissipation monitoring was used. In the absence of unbound NOM, (1) surface modification on either AgNP or silica substrate by different NOM fractions could lead to substantial changes in the extent and kinetics of AgNP aggregation and deposition, and (2) HA has a greater capability to enhance the transport of AgNPs by reducing their aggregation and deposition. With unbound NOM, HA seems to compete more successfully for binding sites on the substrate under electrostatically favorable conditions and formed a steric layer to prevent subsequent deposition of AgNPs. These findings highlighted the importance of NOM fraction in the overall environmental partitioning of AgNPs.