Enhancing flood resilience, including the development of social capacity and early warning systems, in addition to structural measures, is one of the key solutions to mitigating flood damage, which will be more intensified in the future due to climate change. This study was conducted to develop a comprehensive methodology for enhancing flood resilience by improving society-wide disaster literacy under the governance formed through the active participation of all levels of stakeholders in Davao City, Philippines. Specifically, the development of the Online Synthesis System for Sustainability and Resilience, which integrates different disciplines, and the fostering of Facilitators, whose role is to interlink the science community and society, were implemented in a co-designing manner by the collective governance body. The development of basin- and barangay-scale hydrological models realized real-time flood forecasting and climate change impact assessment to identify intensified flood risk under the future climate. Co-designed e-learning workshops were held to foster about thirty Facilitators and help them produce twenty-one risk communication plans and workshop designs for fourteen barangays considering geographic, demographic, economic, and social features that they can utilize for public dissemination related to climate change adaptation to the target audiences in society. This paper presents a practical method to enhance flood resilience, demonstrating that the synthesis of science-based knowledge and human resource development can fill the gaps between the science community and society.