The persistence of silver nanoparticles in aquatic environments and their subsequent impact on organisms depends on key transformation processes, which include aggregation, dissolution, and surface modifications by metal-complexing ligands. Here, we studied how cysteine, an amino acid representative of thiol ligands that bind monovalent silver, can alter the surface chemistry, aggregation, and dissolution of zero-valent silver nanoparticles. We compared nanoparticles synthesized with two coatings, citrate and polyvinylpirrolidone (PVP), and prepared nanoparticle suspensions (approximately 8 μM total Ag) containing an excess of cysteine (400 μM). Within 48 h, up to 47% of the silver had dissolved, as indicated by filtration of the samples with a 0.025-μm filter. Initial dissolution rates were calculated from the increase of dissolved silver concentration when particles were exposed to cysteine and normalized to the available surface area of nanoparticles in solution. In general, the rates of dissolution were almost 3 times faster for citrate-coated nanoparticles relative to PVP-coated nanoparticles. Rates tended to be slower in solutions with higher ionic strength in which the nanoparticles were aggregating. X-ray absorption spectroscopy analysis of the particles suggested that cysteine adsorbed to silver nanoparticles surfaces through the formation of Ag(+I)—sulfhydryl bonds. Overall, the results of this study highlight the importance of modifications by sulfhydryl-containing ligands that can drastically influence the long-term reactivity of silver nanoparticles in the aquatic environment and their bioavailability to exposed organisms. Our findings demonstrate the need to consider multiple interlinked transformation processes when assessing the bioavailability, environmental risks, and safety of nanoparticles, particularly in the presence of metal-binding ligands.