The sustainability in the marine and coastal environment was conceptualized significantly since the Earth Summit in 1992 where Integrated Coastal Zone Management (ICZM) was proposed as one of the solutions that can support the decision makers to work together and provide decisive actions for the better coastal management. A right balance between the socio-economic growth and the environmental protection is the most important goal in the coastal management. In order to achieve the goal, a framework-based strategy, financial planning and policy enforcement must be implemented in the coastal management. Indonesia as one of the archipelagic states has adopted this concept within two Indonesian cooperation laws which were intended to enable the Indonesian government to manage the coastal areas more responsibly and accountably in the aim for the improved environment for future generations. Since the endorsement of those laws, however, the implementation has been lagging and the Indonesia government's focus is rather on the land-based development despite the consequence of the negligence in the coastal management. This is evident in the impact on the coastal environment that is caused by rapid and ill-planned developments in Indonesian coastal regions. As a result, Indonesia already lost four islands associated with Seribu Islands by 1999. It proves that Seribu Islands lack in the policy enforcement and were unnoticed by both the central government and the local government. This paper aims to assess the ecological vulnerability with a focus on coral reefs in Seribu Islands using Geographic Information Systems and Remote Sensing technologies. From the study results, it can be summarized that the urban pressures and pollutants from four main rivers in Jakarta Bay and Banten Province played a significant role in the environmental degradation. Most of the islands associated with Seribu Islands are at risk, if the urban development continues. The vulnerability analysis of Seribu Islands can assist the decision makers to prepare pivotal actions in order to adapt the changes and develop essential recovery programs for the region.