Silver nanoparticles (AgNPs), owing to their effective antimicrobial properties, are being widely used in industry, daily life, and healthcare fields. However, the transformation and bioaccumulation of AgNPs discharged to the aquatic environment have raised extensive concerns about their environmental safety, especially the unintended impacts of AgNPs on microbial ecosystems and associated ecological risks. Toxicity of AgNPs to cyanobacteria has been examined, but the underlying chemical mechanisms of nanotoxicity are still obscure, including how the AgNPs are transported across the complex cell walls of cyanobacteria, and whether the nanoscale size of particles or their decomposition products mediate the cytotoxicity observed.