This paper presents an extension of an existing systematic conceptual design methodology for urban wastewater treatment plants (WWTP) that combines a hierarchical decision process with mathematical modeling (Vidal et al. Ind. Eng. Chem. Res. 2002, 41, 4992−5005). The main contributions of this new approach are (i) to refine criteria selection and quantification used to compare the competing options with different sources of information (dynamic simulation, model-based cost estimations, literature and expert knowledge); (ii) to propose different value functions to normalize the effect of the criteria used; and (iii) to include a visual representation (gray-scale approach) that eases the visualization of the objectives that were not accomplished and of the main handicaps of the evaluated options. Finally a case study, where an activated sludge configuration for carbon and nitrogen removal is selected, and a sensitivity analysis, to show the influence of the context in the final decision, are also presented.