The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance towards them. However, a realistic evaluation of the toxicity of AgNPs in the marine realm is currently missing. Here, we designed a mesocosm experiment to assess the impacts of AgNP exposure on microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the different planktonic components, from viruses up to protists, as well as in the concentration and properties of AgNPs for 33 days. We found that the addition of AgNPs even at a low dose stresses the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition changed significantly. Additionally, lysogeny-related genes increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Moreover, the AgNP transformations in the seawater (increased concentration of dissolved silver ions and decreased AgNP size) and the exposure time significantly affected microbial plankton. Our results highlight that the release of AgNP alters the functioning of the oceanic food web by hampering important viral and bacterial processes.