Indonesian watershed management continues to struggle with various problems caused by natural disasters, particularly hydrometeorological disasters, which are worsened by the effects of climate change. Coordinating and synchronizing the interest of many parties in watershed management with various scenarios of natural conditions is a big challenge in the creation of a healthy and productive watershed. Multiple initiatives have been undertaken, from establishing rules and policies to implementing them and assessing the effects, leading to various lessons being learned for better management. This article presents a study on watershed management in Indonesia and recommends alternative improvements toward healthy and productive watershed management. A combination of a descriptive qualitative analysis of the authors’ experience in various research activities and a critical analysis is used to examine existing conditions and to formulate recommendations for better sustainable management toward a healthy and productive watershed. Most Indonesian watersheds are susceptible to degradation due to numerous threats. The challenges in Indonesian watershed management, including land degradation and climate-induced disasters, lack of synchronization and coordination, limited resources, and anthropogenic factors, have led to decreased watershed health and productivity and hindered effective management. Integrated management, especially at the micro-watershed level, addresses these challenges. Successful integrated watershed management requires community involvement, appropriate management action for specific locations, technological support, regulatory alignment, and stakeholder collaboration to ensure a healthy, productive, and sustainable watershed for present and future generations.