Water system integration can effectively reduce freshwater consumption and minimize wastewater discharge of a water-using system, but integration makes the resultant water network structurally more integrated among process units. Therefore, to design a flexible water allocation network that is easy to control becomes highly desirable. In this Article, a methodology is presented for water allocation network design with process disturbance taken into account. For a new design, the synthesized network structure can guarantee that the water system consumes minimum freshwater under both normal and disturbance conditions and with minimum number of control streams under disturbance. At the same time, the information needed to adjust flow rate under disturbance will be obtained. For an existing water system, an adjustment scheme under disturbance with minimum freshwater consumption for the existing structure will be obtained. The water network designed by the new methodology has the feature of minimum freshwater consumption and high flexibility under disturbance. Some case studies are used to demonstrate the method.