Embodiments of the invention provide methods of removing ions from a feed water stream using a flow-through capacitor and a controller for performing the methods. A target value for a water property concentration or a fixed percent removal of a water property concentration to be removed is established for a treated water stream exiting the flow-through capacitor. A feed value for the water property concentration is measured in a feed water stream entering the flow-through capacitor. An amperage of the flow-through capacitor and a flow rate through the flow-through capacitor is controlled to remove ions from the feed water stream to achieve the desired removal of the water property.