Transformations and long-term fate of engineered nanomaterials must be measured in realistic complex natural systems to accurately assess the risks that they may pose. Here, we determine the long-term behavior of poly(vinylpyrrolidone)-coated silver nanoparticles (AgNPs) in freshwater mesocosms simulating an emergent wetland environment. AgNPs were either applied to the water column or to the terrestrial soils. The distribution of silver among water, solids, and biota, and Ag speciation in soils and sediment was determined 18 months after dosing. Most (70 wt %) of the added Ag resided in the soils and sediments, and largely remained in the compartment in which they were dosed. However, some movement between soil and sediment was observed. Movement of AgNPs from terrestrial soils to sediments was more facile than from sediments to soils, suggesting that erosion and runoff is a potential pathway for AgNPs to enter waterways. The AgNPs in terrestrial soils were transformed to Ag2S (52%), whereas AgNPs in the subaquatic sediment were present as Ag2S (55%) and Ag-sulfhydryl compounds (27%). Despite significant sulfidation of the AgNPs, a fraction of the added Ag resided in the terrestrial plant biomass (3 wt % for the terrestrially dosed mesocosm), and relatively high body burdens of Ag (0.5–3.3 μg Ag/g wet weight) were found in mosquito fish and chironomids in both mesocosms. Thus, Ag from the NPs remained bioavailable even after partial sulfidation and when water column total Ag concentrations are low (<0.002 mg/L).