Rivers substantially contribute to global greenhouse gas emissions, yet emissions from headwater streams are poorly constrained. Here, we report dissolved concentrations of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Andean headwater and piedmont streams in the Napo River basin in Ecuador, part of the Amazon River catchment. Concentrations increased exponentially with elevation decrease between 3990 and 175 m above sea level. Concentration changes scaled with catchment slope, and were attributed to variations in gas transfer velocity, forest cover, inundation extent, and water temperature. We estimate river emissions across the whole Amazon basin using existing data for the lowland Central Amazon. We find that Andean mountainous headwater and piedmont streams are hotspots of CO2 and CH4 emission, with respective areal fluxes being 1.7 and 4.5 higher in headwater streams, and 1.2 and 6.6 higher in piedmont streams than in lowland streams. Together, Andean mountainous headwater and piedmont streams and rivers represented 35% CO2 and 72% CH4 of basin scale integrated fluvial diffusive emissions. Conversely, N2O emissions from headwater and piedmont streams were low compared to lowland streams.