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Shallow tropical bays in the Caribbean, like Orient Bay and Galion Bay in Saint Martin, are often sheltered by coral reefs. In the relatively calm environment behind the reefs, seagrass meadows grow. Together, these ecosystems provide valuable ecosystem services like coastal protection, biodiversity hotspots, nursery grounds for animals and enhancing tourism and fisheries. However, sea-level rise imperils these ecosystems and the services they provide because of changing hydrodynamic conditions, with potential effects on the interdependencies between these ecosystems. By means of a hydrodynamic model that accounts for the interaction with vegetation (Delft3D Flexible Mesh), the impact of sea-level rise (0.87 m in 2100) is investigated for three scenarios of future reef development (i.e. keep-up, give-up and catch-up). If coral reefs cannot keep up with sea-level rise, the wave height and flow velocity increase significantly within associated bays, with the wave height doubling locally in case of eroding reefs in our model simulations. Since the presence of seagrass strongly depends on the hydrodynamic conditions, the response of seagrass to the future hydrodynamic conditions is projected using a habitat suitability model that is based on a logistic regression. The spatial character of the bays determines the response of seagrass. In Orient Bay, which is deeper and partly exposed to higher waves, the seagrass will likely migrate from the deeper parts to shallow areas that become suitable for seagrass because of the surf zone moving landward. In contrast, the conditions for seagrass worsen in Galion Bay for the catch-up and give-up scenario; due to the shallowness of this bay, the seagrass cannot escape to more suitable areas, resulting in significant seagrass loss. It is shown that healthy coastal ecosystems are able to limit the change in hydrodynamic conditions due to sea-level rise. Therefore, preserving these ecosystems is key for ensuring the resilience of shallow tropical bays to sea-level rise and maintaining their ecosystem services. • Sea-level rise intensifies hydrodynamic conditions in shallow tropical bays. • Wave dissipation by coral reefs controls the impact of sea-level rise. • The spatial character of the bay determines the response of seagrass. • Tropical marine ecosystems can mitigate the impact of sea-level rise. [ABSTRACT FROM AUTHOR]