Abstract. Rivers act as a natural source of greenhouse gases (GHGs) that can be released from the metabolisms of aquatic organisms. Anthropogenic activities can largely alter the chemical composition and microbial communities of rivers, consequently affecting their GHG emissions. To investigate these impacts, we assessed the emissions of CO2, CH4, and N2O from Cuenca urban river system (Ecuador). High variation of the emissions was found among river tributaries that mainly depended on water quality and neighboring landscapes. By using Prati and Oregon Indexes, a clear pattern was observed between water quality and GHG emissions in which the more polluted the sites were, the higher were their emissions. When river water quality deteriorated from acceptable to very heavily polluted, their global warming potential (GWP) increased by ten times. Compared to the average estimated emissions from global streams, rivers with polluted water released almost double the estimated GWP while the proportion increased to ten times for very heavily polluted rivers. Conversely, the GWP of good-water-quality rivers was half of the estimated GWP. Furthermore, surrounding land-use types, i.e. urban, roads, and agriculture, significantly affected the river emissions. The GWP of the sites close to urban areas was four time higher than the GWP of the nature sites while this proportion for the sites close to roads or agricultural areas was triple and double, respectively. Lastly, by applying random forests, we identified dissolved oxygen, ammonium, and flow characteristics as the main important factors to the emissions. Conversely, low impact of organic matter and nitrate concentration suggested a higher role of nitrification than denitrification in producing N2O. These results highlighted the impacts of land-use types on the river emissions via water contamination by sewage discharges and surface runoff. Hence, to estimate of the emissions from global streams, both their quantity and water quality should be included.