This report presents the assessment of the Amazon Basin – the largest basin on the planet and also one of the least understood. Although sparsely inhabited, the Basin is subject to extensive anthropogenic impacts through deforestation, mining, hydropower generation and agricultural activities that all have contributed to considerable changes in aquatic habitats and communities. The root causes of habitat and community modification are identified in the Madeira Basin, shared by Brazil, Bolivia and Peru, and potential policy options are presented.