Urban population growth and the expansion of the built environment, pollution, overexploitation of water, inequality in water distribution, and the impacts of climate change in future availability of water, are all elements that jeopardize urban water security. Due to the complexity of urban water systems and their relevance for urban life, a holistic and integrative perspective is therefore needed to address such challenges. In this paper, Urban Water Metabolism (UWM) has been used for comprehensively understanding water (in)security in the City of Puebla (Mexico) and its metropolitan area. Water inflows and outflows have been estimated using a Material Flow Analysis (MFA) method with data either obtained from official sources or simulated with the Monte Carlo method. Our findings show that the UWM configuration in the City of Puebla and its metropolitan area is effective for generating profits to service providers and water related business, yet ineffective to guarantee citizens’ Human Right to Water and Sanitation (HRWS), a right recognized in the Constitution of Mexico. We conclude that to advance towards an inclusive and sustainable provision of water, economic interests must be reconsidered and therefore adjusted so they can be in line with such aspirational socioecological goals. UWM accounting can therefore inform new water governance arrangements, those based on both the best available knowledge and a vibrant participation of all relevant stakeholders.