Summary: Wastewater treatment has become one of the most important environmental problems, especially for the particular case of urban areas. In this work we use numerical simulation, and combine optimal control theory of partial differential equations with multi-objective optimization techniques to formulate and solve this type of problems. Specifically, the main objective of this paper is to detail the mathematical tools that we can use in order to assess in decision making related to determining the sewage depuration intensities in a wastewater treatment system. We show the usefulness of our techniques by solving a realistic problem posed in the estuary of Vigo (NW Spain) with the free software SOS, recently developed by the authors.