CO2 and CH4 fluxes measured in the field, in flowing waters, disconnected pools or dry riverbeds, from the 6 European DRNs, in 3 sampling campaigns, together with associated environmental data for each reach-campaign-habitat. Sediment characterization included: pH, conductivity, humidity, organic matter, carbon and nitrogen content and sediment temperature (only in dry riverbeds). Environmental variables included: flow state, habitat where sample was collected (flowing waters, dry riverbed, isolated pool), air temperature, river wetted width and discharge (only in flowing conditions); water conductivity, temperature, pH, dissolved oxygen (absolute concentration and % saturation) and water nitrate, ammonium and soluble reactive phosphorus (in flowing conditions and isolated pools).