Engineered silver nanoparticles (AgNPs), largely known to act as antimicrobial agents, are increasingly incorporated into consumer products like clothing, medical device and even children’s toys. Such rapid development and widespread usage of AgNPs in these sectors is likely to result in the entry of AgNPs into both natural and engineered systems, which has the potential to disrupt important bacterial processes including those involved in biogeochemical cycling of essential nutrients. While the stability and antibacterial activity of AgNPs have recently drawn considerable attention, the majority of this research to date has been carried out under either aerobic or strictly anaerobic such as ferrogenic, sulfidogenic and methanogenic conditions. Little is known about the geochemistry and microbial toxicity of AgNPs in the environment where nitrate reduction is characterized as the primary terminal electron accepting process, i.e., denitrification, nor is the role of natural organic matter (NOM) involved in this process. Denitrification is an important microbially mediated process that is indispensable for nitrogen cycling in the fundamental biogeochemical processes and nitrogen removal in the conventional wastewater treatment activities. However, equilibrium models have predicted that anoxic oxidation of bulk amorphous Ag(0) to ionic Ag(I) by most dissmilatory nitrate reduction intermediates at the standard state is a thermodynamically favorable reaction. Hence, given that a better understanding of the relationship between engineered nanoparticles and response at the molecular and community levels of microbes is crucial to better predict and interpret the ultimate behavior and adverse impact of these novel materials in the environment, here we propose to conduct thorough, in-depth investigations to study transformation and bactericidal effect of engineered AgNPs under denitrifying conditions. Specifically, by performing microcosm incubation and bench-scale sequencing batch reactor experiments, we will (i) explore the roles of intermediate nitrogen species and NOM in the oxidation and toxicity of AgNPs in the denitrifying cultures/process, (ii) examining the effect of particle size, shape and charge in association with observed AgNP transformation and toxic effect, as well as (iii) characterize the resulting physiological, genetic, enzymatic and microbial community changes. Results of this study may provide insight into the assessment and management on the ecological risk associated with AgNP-exposure in the anoxic environment.