Rapid urbanization and population growth are placing more demands on the world’s natural water resources. New infrastructures are increasing the degree of surface sealing as well as the tendency for urban flooding and water quality degradation. These problems can be counteracted by nature-based solutions (NBS) for urban drainage in developed countries mostly having a temperate climate. Hence, there is a need to develop similar sustainable measures for tropical regions as currently there are no guidelines available. In this study, the multi-criteria decision analysis (MCDA) approach was utilized to identify the best site for NBS in the Asian Institute of Technology (AIT) in Bangkok, Thailand. Then, Personnel Computer Storm Water Management Model (PCSWMM) software was used to develop a numerical model. It was found that the MCDA approach is appropriate to determine the best site for NBS implementation considering different aspects including economic, environmental, and technical ones. The results strongly suggested that Site-1 is a suitable alternative to implement NBS in the AIT campus. It was found that a bioretention system can reduce runoff volume by at least 14% and pollutants by at least 14–20%. The present study will provide a guideline for site selection and development of the NBS model for urban water management in a tropical climate.