The watershed ecosystem is a complex system in which there are numerous transportation and transfer mechanisms of mass and energy. To make management more effective in all national critical watersheds, there needs to be more scientific, evidence-based policymaking that is based on an understanding of the system and mechanisms of the socio-hydrological processes of the watershed. The availability of Decision Support System (DSS) technology can be the appropriate approach to this need because DSS can be an interface between scientific and practical needs (easy-to-use, easy-to-access, user-friendly). However, the availability and implementation of DSS as an important tool in the optimal design of sustainable watershed management in Indonesia are still very limited. This study aims to create a prototype DSS that practitioners and policymakers can use to identify priority areas and optimize technical solutions for controlling surface runoff and soil erosion at various scales in the internal watershed. Herein, the spatial-based numerical modeling system and process mechanism; the database and knowledge; and the Graphical User Interface (GUI) are the three main components that have been used as a framework for model-based DSS development. A distributed rainfall-runoff-erosion model (EcoHydro) is the main engine of DSS for spatially quantifying dimensions of hydrological responses, erosion rate, and sediment production according to the user’s specifications and providing design options for control measures of them. The upper Citarum river basin in West Java, which is a critical and first national priority watershed, has been selected as the case study for DSS development and to demonstrate its application. Furthermore, the resulting DSS can later be developed for use in watersheds and other nationally critical lakes.