A continuous-flow system utilizes microwave heating to sterilize water and to thermally inactivate endotoxins produced in the sterilization process. The system is designed for use in converting potable water to medical-grade water. Systems like this one could be used for efficient, small-scale production of medical-grade water in laboratories, clinics, and hospitals. This system could be adapted to use in selective sterilization of connections in ultra-pure-water-producing equipment and other equipment into which intrusion by microorganisms cannot be tolerated. Lightweight, portable systems based on the design of this system could be rapidly deployed to remote locations (e.g., military field hospitals) or in response to emergencies in which the normal infrastructure for providing medical-grade water is disrupted. Larger systems based on the design of this system could be useful for industrial production of medical-grade water.