This work tested the antimicrobial activity of three different biogenic silver nanoparticles (AgNPs) against Escherichia coli (E. coli) for water disinfection processes. The influence of different AgNP capping or stabilizing agents (e.g., protein or carbohydrate capped) and the use of ultraviolet (UV) radiation on the disinfection process were also assessed. The use of UV radiation was found to enhance the antimicrobial effects of AgNPs on E. coli. The antibacterial effects of AgNPs depended on the type of the capping biomolecules. Protein-capped nanoparticles showed greater antimicrobial effects compared with carbohydrate-capped (cellulose nanofibers, CNF) nanoparticles. Those capped with the fungal secretome proteins were the most active in E. coli inactivation. The least E. coli inactivation was observed for CNF-capped AgNPs. The size of the tested AgNPs also showed an expected effect on their anti-E. coli activity, with the smallest particles being the most active. The antimicrobial effects of biogenic AgNPs on E. coli make them an effective, innovative, and eco-friendly alternative for water disinfection processes, which supports further research into their use in developing sustainable water treatment processes.