Encouraging the implementation of non-conventional water resources (NCWR) is a fundamental strategy to face the future challenges due to urban population growth and resource scarcity. The implementation of a systematic process of Cost Benefit Analysis (CBA) offers reliable economic indicators to support decision makers in taking actions shifting towards NCWR. While infrastructure costs are directly estimated, while the benefits depend upon the considered stakeholders and require a tough estimation of the achieved ecosystem services. This research provides a framework for CBA analysis adopting NCWR at municipal level. The framework has been then applied to two case studies in Milan focused on the exploitation of shallow groundwater, where the obtained economic indicators has stressed out the importance of considering a complete benefits analysis that could support incentive policies on shifting part of the financial benefits to direct users leading to benefits for the whole community.