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In 1997 scientists proposed an agenda for biogeochemical research in river corridors of the Amazon basin to both identify gaps in knowledge and to outline a possible approach to filling those gaps. Most previous research in the Amazon had focused on natural processes with a majority of effort on the main stem and its largest tributaries; much less was known about the small river corridors at both the micro (<100 ha) and meso (<100,000 ha) scale or the riparian forests or floodplains around these rivers. In addition, although many potential impacts on rivers and floodplains from anthropogenic land cover or land use conversion were proposed little empirical data were available. A nested sampling design from micro- to macro-scale was proposed. Over the intervening 13 years of research as part of the Largescale Biosphere Atmosphere project in Brazil much new information has been gained. Many studies at the small watershed scale demonstrated clear impacts on stream water flow paths from groundwater to surface water due to forest loss. In addition, processes controlling chemical composition were advanced including surface interflow and in-stream processing. At the meso-scale distributed hydrologic models successfully captured human influence on river process. At the macro-scale carbon processing from land to water was further elucidated, particularly with the extent and activity of flood inundated areas. The lag in response from small watershed to the macro-basin remains a pressing question. Similarly, the role of impoundments or climate change on flood stage and floodplain function needs further consideration.