Although mountains often constitute only a small fraction of river basin area, they can supply the bulk of transported materials and exert strong regulatory controls on the ecological characteristics of river reaches and floodplains downstream. The Amazon River exemplifies this phenomenon. Its muddy waters and its expansive and highly productive white-water floodplains are largely the products of forces originating in distant Andean mountain ranges. The Amazon's character has been shaped by these influences for more than 10 million years, and its present form and host of diverse organisms are adapted to the annual and interannual cycles of Andean inputs. Although the Andes constitute only 13% of the Amazon River basin, they are the predominant source of sediments and mineral nutrients to the river's main stem, and Andean tributaries form productive corridors extending across the vast Amazonian lowlands. Many of the Amazon's most important fish species rely on the productivity of Andean tributaries and main-stem floodplains, and annual fish migrations distribute Andean-dependent energy and nutrient resources to adjacent lower-productivity aquatic systems. Mountain-lowland linkages are threatened, however, by expanding human activities in the Andean Amazon, with consequences that are eventually felt thousands of kilometers away.