It is a great challenge to monitor the physical and chemical transformation of nanoparticles at environmentally relevant concentration levels, mainly because the commonly used techniques like dynamic light scattering and transmission electron microscopy are unable to characterize and quantify trace level nanoparticles in complex matrices. Herein, we demonstrate the on-line coupled system of hollow fiber flow field-flow fractionation (HF5), minicolumn concentration, and inductively coupled plasma mass spectrometry (ICPMS) detection as an efficient approach to study the aggregation and chemical transformation of silver nanoparticles (AgNPs) and ionic Ag species in the aqueous environment at ng/mL levels. Taking advantage of the in-line dialysis of HF5, the selective capture of Ag(I) species by the resin in minicolumn, and the high selectivity and sensitivity of ICPMS detection, we recorded the aggregation of 10 ng/mL AgNPs in complex matrices (e.g., NOM, Na+/Ca2+), revealing an interesting tiny AgNPs formation process of photoreduction of trace level Ag(I) that is different from larger AgNPs generated at high concentration of Ag(I) by accurate characterization and respectively identifying and quantifying new thiol-complexed Ag(I) and residual Ag(I) in the intertransformation of Ag(I) and AgNPs in domestic wastewater by simultaneously detecting the S and Ag signals via ICPMS.