Methods and systems for electrochemically processing microfeature workpieces are described herein. In one embodiment, a process for electrochemically treating a surface of a plurality of microfeature workpieces in an electrochemical treating chamber that includes a processing unit separated from an electrode unit by an ion-permeable barrier is described. The process involves an idle stage wherein during the idle stage, processing fluid components are prevented from transferring between the first processing fluid and the second processing fluid. The described system includes a flow control system for controlling the flow of processing fluid to achieve separation of a processing fluid from the barrier during the idle stage.