An important increase in flood risk levels is expected in future decades in many areas around the globe. In addition, the traditional approaches for flood management offer options with low sustainability. As a response, the use of non-traditional drainage measures, also called green infrastructures, has been increasingly suggested in the last years. One important reason for their increasing popularity has been the co-benefits that they offer to the environment. The development of an efficient planning for sustainable urban drainage systems is a complex process that needs the involvement of multiple stakeholders. Moreover, the measures to be adopted should be evaluated considering their potential to achieve multiple benefits related to human well-being, rather than just to flood risk management. In this work, we propose a framework for the selection of green infrastructures on the basis of a co-benefits analysis. The aim is to include the achievement of co-benefits and human well-being into decision-making for flood management, considering the stakeholders’ perceptions to define the most important benefits to be enhanced. The application of the framework presented here to a case study in Ayutthaya, Thailand, shows the importance of including different stakeholder’s opinions. In addition, it shows that decision makers should consider locally defined co-benefits as well as flood risk reduction when defining which green infrastructures to apply.