A rapid and efficient micromotor-based bacteria killing strategy is described. The new antibacterial approach couples the attractive antibacterial properties of chitosan with the efficient water-powered propulsion of magnesium (Mg) micromotors. These Janus micromotors consist of Mg microparticles coated with the biodegradable and biocompatible polymers poly(lactic-co-glycolic acid) (PLGA), alginate (Alg) and chitosan (Chi), with the latter responsible for the antibacterial properties of the micromotor. The distinct speed and efficiency advantages of the new micromotor-based environmentally friendly antibacterial approach have been demonstrated in various control experiments by treating drinking water contaminated with model Escherichia coli (E. coli) bacteria. The new dynamic antibacterial strategy offers dramatic improvements in the antibacterial efficiency, compared to static chitosan-coated microparticles (e.g., 27-fold enhancement), with a 96% killing efficiency within 10 min. Potential real-life applications of these chitosan-based micromotors for environmental remediation have been demonstrated by the efficient treatment of seawater and fresh water samples contaminated with unknown bacteria. Coupling the efficient water-driven propulsion of such biodegradable and biocompatible micromotors with the antibacterial properties of chitosan holds great considerable promise for advanced antimicrobial water treatment operation.