In the face of rising the seas, relying solely on seawalls and other reinforced coastlines is unsustainable due to the high costs associated with their construction and upkeep and unforeseen effects on habitats. Restoring and conserving coastal habitats can be more affordable, long-term solutions for protecting the coast. Yet, basic knowledge about where, how, and for whom habitats decrease the risk of coastal disasters is typically lacking from decision-makers. This study investigates how climate change may affect coastal areas and how natural coastal habitats may help protect them. We studied two small tropical islands, Bintan and Seribu Islands, Indonesia. The research applied the InVEST Coastal Vulnerability model to calculate the hazard index. To assess the effect on the vulnerable population, a grid system for the coastal population was created and overlaid with the hazard index. The comprehensive analysis indicates that if the coastal habitat is lost in the future, Bintan and Seribu Islands will face a severe threat from rising sea levels, with 96% and 63% of the inhabitants being highly exposed to climate hazards. Furthermore, the model shows that preserving natural coastal habitats by 2040 could help protect approximately 104 and 17 km of coastline areas in Bintan and Seribu Islands, respectively. Ecosystems offer safeguards to certain thinly inhabited, distant coastal villages, certain of those with a large, vulnerable population. Thus, this study highlights that natural coastal habitat is essential in climate change adaptation. Enhancing and safeguarding these natural habitats is crucial for mitigating climate-related hazards and ensuring community resilience.