We measured the emission of carbon dioxide (CO₂) and methane (CH₄) from different sites at the river Elbe in Germany over 3 days to find out what is more important for quantification: small-scale spatial variability or diurnal temporal variability. We found that CO₂ emissions were very different between day and night, while CH₄ emissions were more different between sites. Dried out river sediments contributed to CO₂ emissions, while the side areas of the river were important CH₄ sources.