The objective of this paper is to present the development of a decision support system (DSS) that generates flow diagrams in wastewater treatment plants (WWTP). The proposed DSS is based on a hierarchical decision approach that breaks down a complex design problem into a series of issues easier to analyze and to evaluate. For each one of these issues, three levels of abstraction are defined (units, submeta-units and meta-units) modifying their degree of engineering detail and thus facilitating the decision maker being focused at each design step. The generation of the flow diagrams is carried out by means of the interaction of two knowledge bases (KB). The first knowledge base (S-KB) summarizes the main features of the different treatment technologies i.e, removal efficiency, costs, process reliability. The second (C-KB) contains information about the degree of compatibility amongst the different technologies i.e. high, low, non-compatible. Both S-KB and C-KB are linked to another data-base (E-KB) with additional information about legislation and special requirements. As a result it is possible to further reduce the number of alternatives and finally decrease the size of the design responses surface. The proposed DSS allows the generation of different WWTP flow diagram: i) including conventional and innovative treatment alternatives, ii) exploring multiples technological combinations, iii) avoiding the consideration of treatment alternatives that a high levels of abstraction resulted to be undesirable iv) offering a customized water treatment scheme according to a set of design requirements and initial conditions and v) finally facilitating the incorporation of different evaluation methods to select the alternative that satisfies the most the different design objectives.