Sustainably maintaining the densely populated upland plains of Madagascar as operationally safe spaces for the food security of the nation and the urban growth of its capital city, Antananarivo, hinges critically on avoiding crop and infrastructure destruction by their through-flowing rivers. The flood regime, however, is also a function of two ‘slow’ variables hitherto undocumented: tectonic subsidence regime, and floodplain sedimentation rate. From a radiocarbon-dated chronostratigraphy and environmental history of the sediment sequences in three of Madagascar's semi-enclosed upland basins (Antananarivo, Ambohibary, and Alaotra), we quantify and compare how the precarious equilibrium between the two variables entails differentials in accommodation space for sediment and floodwater. Results show that all these plains have been wetlands for at least 40,000 years, but that the Antananarivo Basin is the most vulnerable because the imbalance between sedimentation and subsidence is the largest. Although the tectonic regime and the endemic forms of gully erosion that occur in the catchments are beyond human control, we advocate that flood mitigation strategies should focus on the natural grassland savanna, which makes up most of the contributing areas to surface runoff in the watersheds. Pastoralists are persistently left out of rural development programmes, yet the rangelands could benefit from the introduction of multi-purpose grasses and legumes known to withstand high stocking rates on poor soils while combining the benefits of nutritiousness, fire and drought resistance, with good runoff-arrest and topsoil-retainment abilities. Future-proofing Madagascar's upland grainbaskets and population centres thus calls for joined-up action on the sediment cascade, focusing on soil and water sequestration through integrated watershed management rather than on hard-defence engineering against overflowing rivers on the plains, which has been the costly but ineffectual approach since the 17th century.