Antimicrobial compositions for killing or deactivating microbes, such as viruses, bacteria, or fungi, include metal nanoparticles, a carrier, and a plurality of metal nanoparticles. The nanoparticles can be selected to have a particle size and particle size distribution to selectively and preferentially kill one of a virus, a bacterium, or a fungus. Antiviral compositions can include nanoparticles having a particle size of 8 nm or less, 1-7 nm, 2-6.5 nm, or 3-6 nm (or up to 10 nm for Ebola virus). Antibacterial compositions can include nanoparticles having a particle size of 3-14 nm, 5-13 nm, 7-12 nm, or 8-10 nm. Antifungal compositions can include nanoparticles having a particle size of 9-20 nm, 10-18 nm, 11-16 nm, or 12-15 nm. Exemplary methods of killing or deactivating microbes include: (1) applying an antimicrobial composition to a substrate containing microbes, and (2) the antimicrobial composition killing or deactivating the microbes.