Water scarcity presents a pressing and lasting challenge to many large cities, necessitating adaptations in urban water systems. Developing reliable water resources is crucial for enhancing water security, yet concerns regarding costs and environmental impacts persist. To address this, we have developed an integrated framework that combines life cycle assessment (LCA), quantitative microbial risk assessment (QMRA), and life cycle costing (LCC) for evaluating the environmental, public health, and economic impacts of water systems. Our approach culminates in a unified monetary representation encapsulating the overall life-cycle costs of the urban water system borne by all stakeholders. City-wide and district-level water systems in Hong Kong were analyzed to demonstrate the benefits of this integrated LCA-QMRA-LCC approach over individual assessments. By quantifying both private and external costs (e.g., environmental and health impacts), we found that the external costs can exceed 50 % of the private costs in both cases, which would potentially influence the decision-making outcomes. Notably, for the district-level study that compared the use of seawater and reclaimed water for toilet flushing, disparities were unveiled between the individual and integrated assessments, underscoring the necessity of a broad LCA-QMRA-LCC framework. This research equips decision-makers with a comprehensive analytical tool, addressing concerns across a broader spectrum of stakeholders and fostering sustainable and costeffective urban water management.