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<p>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 CO<span class="inline-formula">₂</span> and CH<span class="inline-formula">₄</span> fluxes from a 1 km long reach of the lowland river Elbe in Germany over 3 d to establish which factor is more relevant to be taken into consideration: small-scale spatial variability or short-term temporal variability of CO<span class="inline-formula">₂</span> and CH<span class="inline-formula">₄</span> fluxes.</p> <p>GHG emissions from the river reach studied were dominated by CO<span class="inline-formula">₂</span>, 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 CO<span class="inline-formula">₂</span> fluxes were similar at different habitats, while aquatic CH<span class="inline-formula">₄</span> fluxes were higher at the side of the river. Artificial structures to improve navigability (groynes) created still water areas with elevated CH<span class="inline-formula">₄</span> fluxes and lower CO<span class="inline-formula">₂</span> fluxes. CO<span class="inline-formula">₂</span> fluxes exhibited a clear diurnal pattern, but the exact shape and timing of this pattern differed between habitats. By contrast, CH<span class="inline-formula">₄</span> fluxes did not change diurnally. Our data confirm our hypothesis that spatial variability is especially important for CH<span class="inline-formula">₄</span>, while diurnal variability is more relevant for CO<span class="inline-formula">₂</span> 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.</p>