Nanomaterials could be modified with various coatings which could modulate their behavior in the environment, bioavailability and toxicity. The purpose of this study was to determine if the selected coatings of silver nanoparticles (nAg) could influence the fate, bioavailability, and toxicity toward suspension feeding freshwater mussels, Elliptio complanata. Mussels were exposed for 96 h to 50 μg/L of nAg with the following surface coatings: citrate, silicate (Si), polyvinylpyrrolidone (PVP), and branched polyethylenimine (bPEI). After the exposure period, mussels were analyzed for total Ag, resistance to air emersion, oxidative stress, genotoxicity, and autophagosome protein uptake (protein ubiquitinylation) in gills and digestive glands. The data revealed that citrate- and PVP-coated nAg were 2 times more abundant in the digestive gland compared to bPEI- and Si-coated nAg with estimated bioaccumulation factors between 5 and 10. The data revealed that tissue Ag levels were closely associated with air survival time, weight loss during air exposure, DNA strand breaks, LPO, and protein-ubiquitin levels in the digestive gland. The data supports the hypothesis that the coatings could influence bioavailability and toxicity in freshwater mussels.