The future of coastal wetlands and their ecological value depend on their capacity to adapt to the interacting effects of human impacts and sea-level rise. Even though extensive wetland loss due to submergence is a possible scenario, its magnitude is highly uncertain due to limited understanding of hydrodynamic and bio-geomorphic interactions over time. In particular, the effect of man-made drainage modifications on hydrodynamic attenuation and consequent wetland evolution is poorly understood. Predictions are further complicated by the presence of a number of vegetation types that change over time and also contribute to flow attenuation. Here, we show that flow attenuation affects wetland vegetation by modifying its wetting-drying regime and inundation depth, increasing its vulnerability to sea-level rise. Our simulations for an Australian subtropical wetland predict much faster wetland loss than commonly used models that do not consider flow attenuation.