Seagrass meadows provide valuable ecosystem services of coastal protection and chemical habitat formation that could help mitigate the impact of sea level rise and ocean acidification. However, the intensification of hydrodynamic forces caused by sea level rise, in addition to habitat degradation threaten the provision of these ecosystem services. With quantitative field measurements of the coastal protection and chemical habitat formation services of seagrass meadows, we statistically model the relationships between hydrodynamic forces, vegetation density and the provision of these ecosystem services. Utilising a high-resolution hydrodynamic model that simulates end of the century hydrodynamic conditions and three scenarios of coral reef degradation (i.e., keep up, remain or loss) we quantify how the environmental conditions within a tropical bay will change given changes to the provision of ecosystem services. Our study shows that increasing hydrodynamic forces lead to a seafloor made up of a larger grain size that is increasingly unstable and more vulnerable to erosion. The loss of a fringing reef leads to larger hydrodynamic forces entering the bay, however, the 0.87 m increase in depth due to sea-level rise reduces the bed shear stress in shallower areas, which limits the change in the ecosystem services provided by the current benthic seagrass meadow. Loss of seagrass constitutes the greatest change in a bay ecosystem, resulting in the sediment surface where seagrass existed becoming unstable and the median sediment grain size increasing by 5-7 %. The loss of seagrass also leads to the disappearance of the unique fluctuating chemical habitat, which leaves the surrounding community vulnerable to ocean acidification. A reduction or complete loss of these ecosystem services would impact the entire community assemblage while also leaving the surrounding coastline vulnerable to erosion, thus exacerbating negative effects brought about by climate change.