A method for reprocessing a medical device uses a medical device processor with an enclosure for holding the medical device. The enclosure also has a reservoir containing a disinfectant, a water source, and a mixing chamber that retains the medical device. The method delivers disinfectant from the reservoir to an internal channel of the medical device, and further delivers water from the water source to the mixing chamber. A flow sensor is operable to monitor the disinfectant delivered to the internal channels of the medical device.
