The Natural Environment Research Council funded, Amazon Integrated Carbon Analysis (Amazonica) project, was undertaken to refine Amazon basin carbon balance by combining various different types of quantification strategies, ranging from biomass plots to eddy covariance studies and air craft measurements of the atmospheric composition. Amazonica work package 5, which generated these data, was responsible for quantifying the role of aquatic carbon export, which is often overlooked. In the more fertile Western part of the Amazonian basin, Madre de Dios region, Peru, two streams and two rivers were sampled from February 2011 May 2012. Water chemistry (pH, conductivity and dissolved oxygen) and stage height were measured continuously in two small streams and as spot measurements in two rivers. Flow velocity was measured during campaigns in the streams to establish rating curves. In these drainage systems the concentration and composition of fluvial carbon (dissolved inorganic carbon and the stable carbon isotopic composition of DIC, dissolved organic carbon and particulate organic carbon), aquatic CO2 efflux, and nutrient concentrations were collected during three field campaigns targeting different seasons. During the third field campaign the carbon and nutrient content of rainfall fractions were studied. The stream samples were taken to understand the hydrological controls on the carbon concentrations and fluxes during different flow conditions. The rainfall fraction samples were taken to understand the nutrient and carbon delivery in rainwater as well as leaching from tree canopies, stems and from the soil surface. The data collection was carried out as part of the Natural Environment Research Council (NERC) funded Amazonica project (NE/F005482/1).