Near-shore coral reef systems are experiencing increased sediment supply due to conversion of forests to other land uses. Counteracting increased sediment loads requires an understanding of the relationship between forest cover and sediment supply, and how this relationship might change in the future. Here we study this relationship by simulating river flow and sediment supply in four watersheds that are adjacent to Madagascar's major coral reef ecosystems for a range of future climate change projections and land-use change scenarios. We show that by 2090, all four watersheds are predicted to experience temperature increases and/or precipitation declines that, when combined, result in decreases in river flow and sediment load. However, these climate change-driven declines are outweighed by the impact of deforestation. Consequently, our analyses suggest that regional land-use management is more important than mediating climate change for influencing sedimentation of Malagasy coral reefs.