The city of Puebla is a mid-sized Mexican city facing multiple water-related challenges, from overexploitation of water sources and extreme pollution of rivers to water conflicts and contestation processes due to the privatization of water supply. Due to the complexity of urban water systems and their relevance for urban life, a holistic and integrative perspective is therefore needed to inform policymakers addressing such challenges. In this paper, Urban Water Metabolism (UWM) has been used to offer a comprehensive understanding of current water insecurity in the City of Puebla and its metropolitan area. Water inflows and outflows have been estimated using the 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 for service providers and water-related businesses, yet ineffective for guaranteeing 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 long-term provision of water, economic goals must follow socio-ecological goals, not the other way around. We consider UWM accounting useful for informing policy and decision-making processes seeking to build a new water governance based on both the best available knowledge and inclusive and vibrant social participation.