Rapid urban growth, particularly in the Global South, has led to uncontrolled land-use change, environmental degradation, natural resource depletion, and increasing expenditures for infrastructure provision. This study uses a case study approach, aiming to determine how rapid urban growth in Jakarta should be managed and translated into land use planning and regulation in order to alleviate environmental degradation and flood risk while providing equitable, resilient, and sustainable land and water resources. Furthermore, the study discusses the opportunity of Low Impact Development (LID) as an alternative approach to addressing flooding, land and water scarcity, and increasing infrastructure costs in Jakarta. The study found that rapid urban growth in Jakarta creates a pattern of concentrated residential clusters in its outskirts and satellite cities, and reducing green open spaces and water catchment areas. Simultaneously, commercial clusters proliferate in the core city and push low-income communities to disaster-prone or underserved areas. This study argues that rapid urban growth should be managed using a sustainable urban growth paradigm, which regulates development based on the barriers and opportunities provided by the natural environment and promotes the adoption of nature-based solutions. Jakarta’s sustainability also depends on how the government addresses the overlooked need of underserved communities. Organic development revolving around low-income communities should be considered in creating comprehensive, consistent, and equitable spatial regulations and urban policies. The complexity of Jakarta’s urban problems due to rapid growth, flood risk, and limited water resources will not be solved if the local government only uses structural solutions. Water and land use management in Jakarta can be improved through integrated land planning and design approaches such as low impact development (LID) performed with enhanced public participation. Regional collaboration, integrated governance, reliable land use data, and enhanced law enforcement are needed to overcome issues that cross administrative boundaries like flooding and water scarcity.