This study presents a systematic conceptual design methodology for urban wastewater treatment plants (WWTP) that combines a hierarchical decision process with the mathematical modeling of the WWTP. An existing WWTP (Granollers WWTP, Spain) was chosen as a case study to apply the proposed design methodology. The design methodology carries with it three sets of advantages: (1) the systematic evaluation of the different alternative designs with respect to a set of criteria, (2) the integration of mathematical modeling in the evaluation of the different alternative designs, and (3) the maintenance of a record of the design process. Finally, a redesign example that shows how the records of a design process can be used to identify the decisions affected by a change in the design objectives is also presented.