The rivers flowing into the Western Indian Ocean have steep headwater gradients and carry high sediment loads. In combination with strong tides and seasonal rainfall, these rivers create dynamic deltas with biodiversity-rich and productive ecosystems that, through flooding, have sustained indigenous use systems for centuries. However, river catchments are rapidly changing due to deforestation. Hydropower dams also increasingly alter flood characteristics, reduce sediment supply and contribute to coastal erosion. These impacts are compounded by climate change. Altogether, these changes affect the livelihoods of the delta users. Here, based on prior works that we and others have conducted in the region, we analyse the drivers of these hydro-ecological changes. We then provide recommendations for improved dam design and operations to sustain the underlying delta-building processes, the ecosystem values and the needs of the users.