A treatment system provides treated or softened water to a point of use by removing at least a portion of any undesirable species contained in water from a water source. The treatment system can be operated to reduce the likelihood of formation of any scale that can be generated during normal operation of an electrochemical device. The formation of scale in the treatment system, including its wetted components, may be inhibited by reversing or substituting the flowing liquid having hardness-causing species with another liquid having a low tendency to produce scale, such as a low LSI water. Various arrangements of components in the treatment system can be flushed by directing the valves and the pumps of the system to displace liquid having hardness-causing species with a liquid that has little or no tendency to form scale.