Data-set consists of two files: - data_ghgs.xlsx : Time-stamped and georeferenced data-set of the partial pressure of CO2 (pCO2 in ppm), dissolved CH4 concentration (CH4 in nmol/L), dissolved N2O concentration (N2O in nmol/L), specific (Sp.) conductivity (in µS/cm), water temperature (in °C), dissolved nitrate concentration (NO3- in µmol/L), dissolved nitrite concentration (NO2- in µmol/L), and dissolved ammonia concentration (NH4+ in µmol/L) in the rivers and streams of the Napo River basin in Ecuador (October 2018 and 2019, January 2019 and 2020, April 2019 and 2021, July 2019 and 2020). Gas measurements were made by headspace equilibration directly in the field with a infra-red gas analyser for CO2 and in the lab with a gas chromatograph for CH4 and N2O. NO3-, NO2- and NH4+ were measured with standard colometric procedures. Sampling and analytical protocols are provided here https://doi.org/10.5194/bg-16-3801-2019 - RiverATLAS.xlsx: hydro-environmental data for the sampled streams extracted from RiverATLAS (https://www.nature.com/articles/s41597-019-0300-6). Data codes and units are available here: https://data.hydrosheds.org/file/technical-documentation/HydroATLAS_TechDoc_v10_1.pdf First column of each of the two files provides station ID allowing to merge both data-sets.