Nowadays, microorganisms, including bacteria and viruses, are regarded as new environmental pollutants and pose serious threats to public health. Yet, traditional disinfection approaches for bacteria and viruses are generally ineffective. Furthermore, they exhibit the disadvantages of high-energy consumption, environmental pollution, high cost, and toxic byproduct generation. In this respect, nanomaterials display promising antimicrobial capabilities due to their unique properties and provide solutions to the abovementioned issues. Herein, recent progress in the development of 2D nanomaterials displaying antimicrobial capabilities is highlighted. The structures, morphologies, and performances of essential metal, graphene, and nitride-based 2D antibacterial nanomaterials are summarized in detail. In addition, possible antimicrobial mechanisms and the relationship between structure and antimicrobial efficiency are elaborated.