The prevalence of silver nanoparticles (AgNPs) requires a comprehensive understanding of their biological impacts especially in marine and estuarine environments. Nevertheless, the background Ag concentration in organisms may impede the accuracy of Ag detection if the net accumulated Ag is low over a short exposure period. Here, a radio-synthesizing method was employed to trace the behavior of AgNPs with two sizes (15 and 60 nm) and two coatings (humic acid and citrate) in an estuarine oyster Crassostrea hongkongensis. This method was sensitive to detect the bioaccumulation and depuration of AgNPs in the oysters over a short period of exposure, which was necessary given the significant changes of particle aggregation in saline water environments. Through radioactive AgNP tracing and biokinetic modeling, we for the first time demonstrated the differential uptake mechanisms of different-sized AgNPs in oysters. Specifically, the ingestion of particles dominated the uptake of 60 nm AgNPs, whereas dermal uptake and ingestion contributed equally to 15 nm AgNPs. Surface coating (humic acid vs citrate) did not significantly affect the uptake of AgNPs by the oysters. The depuration of AgNPs from the oysters was relatively faster than that for the Ag ion. The digestive gland was the key detoxification organ of AgNPs with the greatest loss of Ag by the end of depuration. The findings of this study provide fundamental knowledge for nano-specific risk assessment in marine and estuarine environments.