Greenhouse gas (GHG) emissions from rivers are globally relevant, but quantification of these emissions comes with considerable uncertainty. Quantification of ecosystem-scale emissions is challenged by both spatial and short-term temporal variability. We measured spatio-temporal variability of CO2 and CH4 fluxes from a 1km long reach of the lowland river Elbe in Germany over 3d to establish which factor is more relevant to be taken into consideration: small-scale spatial variability or short-term temporal variability of CO2 and CH4 fluxes. GHG emissions from the river reach studied were dominated by CO2, and 90% of total emissions were from the water surface, while 10% of emissions were from dry fallen sediment at the side of the river. Aquatic CO2 fluxes were similar at different habitats, while aquatic CH4 fluxes were higher at the side of the river. Artificial structures to improve navigability (groynes) created still water areas with elevated CH4 fluxes and lower CO2 fluxes. CO2 fluxes exhibited a clear diurnal pattern, but the exact shape and timing of this pattern differed between habitats. By contrast, CH4 fluxes did not change diurnally. Our data confirm our hypothesis that spatial variability is especially important for CH4, while diurnal variability is more relevant for CO2 emissions from our study reach of the Elbe in summer. Continuous measurements or at least sampling at different times of the day is most likely necessary for reliable quantification of river GHG emissions.