In the past years, alternative drainage approaches have emerged, such as Sustainable Urban Drainage Systems (SUDS), to prevent run-off and flooding impacts on the most vulnerable zones of the cities. These systems not only provide the benefit of water regulation but also promote other types of ecosystem services. Several studies have developed optimization tools to assist SUDS selection, location, and design. However, they do not consider a comprehensive set of ecosystem services (e.g., provision, regulation, cultural, and support services). This research proposes a flexible and adaptable methodology to incorporate SUDS in different stages of urban projects using a multi-objective optimization technique to minimize run-off, maximize ecosystem services and minimize cost. The methodology comprises four phases: (1) the preliminary analysis of ecosystem services potentially generated by each SUDS type, (2) the priority and opportunity index quantification, (3) the physical feasibility analysis, and (4) the multi-objective optimization tool implementation. The methodology was successfully applied to three different urban areas of Bogotá city (Colombia). Results evidence that the interaction of the budget constraints and the available area restrict the potential benefits of SUDS implementation. These results are helpful to support different urban planning stages.