An estimated 933 million people worldwide face water scarcity in urban environments with marginalized low-income populations. Rainwater harvesting has been proposed as an adaptable mitigation strategy to reduce water scarcity in those environments. As a case study, the present work proposes the implementation of a rainwater harvesting program aimed at the mitigation of water scarcity in highly vulnerable areas within the Metropolitan Area of Guadalajara, Mexico. The program was developed and structured based on an innovative strategy with replicable multicriteria characterization and prioritization, to allocate the rainwater harvesting systems in areas with a high sensitivity to water scarcity. The areas were selected based on territorial, hydrologic, and social parameters. The prioritization methodology was successfully applied for the selection of clusters for the allocation of domestic rainwater harvesting systems. A total of 4550 rainwater harvesting units were implemented leading to an estimated total yearly capture of 163,444.88 m³. Based on surveys, a reduction of 44% in the time spent water-gathering as well as a 14.2% reduction in waterborne diseases was observed in the participant households after 6 months of the systems' implementation. The developed prioritization methodology offers an alternative for science-based resource allocations aimed at the resolution of specific complex challenges. This methodological approach could be adapted and replicated for other spatial-based decision-making and public policy applications. The implemented program offered an alternative for water scarcity mitigation in an urban environment and its application showed potential to improve the quality of life of the population, who benefited by increasing water access and availability.