Abstract: Methods of operating an electrochemical separation device is disclosed. The methods include operating the electrochemical separation device in an active mode until the resistance reaches a predetermined threshold, regenerating the electrochemical separation device in a passive mode until the resistance reaches a predetermined threshold, and resuming operation of the electrochemical separation device in the active mode. The methods also include operating the electrochemical separation device in an active mode for a predetermined period of time, regenerating the electrochemical separation device in a passive mode for a predetermined period of time, and resuming operation of the electrochemical separation device in the active mode. Water treatment systems include the electrochemical separation device and a control module are also disclosed. Methods of facilitating operation of the electrochemical separation device by providing a control sequence are also disclosed.