The wide use of silver nanoparticles (AgNPs) leads to the increasing release of AgNPs into the environment. Dissolved organic matter (DOM) is a key factor affecting the behaviors and fate of AgNPs in the aquatic environment. However, the mechanisms for the DOM-mediated transformations of AgNPs are still not fully understood. In this study, we investigated the persistence of AgNPs in the aquatic environment in the presence of different concentrations of humic acid (HA) over periods of time up to 14 days. The Ag species were monitored and characterized by absorption spectrometry, transmission electron microscopy (TEM), inductively coupled plasma mass spectrometry (ICP-MS), and multicollector ICP-MS (MC-ICP-MS). Results showed that the long-term persistence of AgNPs in HA-containing water was determined by two critical concentrations of HA. When the HA concentration exceeded a lower critical value, AgNPs could be persistent in the solution, and a large number of AgNPs were formed secondarily from the HA-induced reduction of the Ag+ ions released from the primary AgNPs, causing a redistribution of the particle size. With the HA concentration above a higher critical value, AgNPs could persist in the solution without a significant change in particle size. Notably, we used Ag isotope fractionation to investigate the transformation mechanism of AgNPs. The natural isotopic analysis by MC-ICP-MS revealed that the size redistribution of AgNPs caused significant Ag isotope fractionation, which gave additional evidence for the proposed mechanisms. This study provides new insights into the environmental fate of engineered AgNPs and highlights the usefulness of stable isotope fractionation in environmental nanotechnology.