Rivers are significant sources of greenhouse gases (GHGs; e.g., CH₄ and CO₂); however, our understanding of the large-scale longitudinal patterns of GHG emissions from rivers remains incomplete, representing a major challenge in upscaling. Local hotspots and moderate heterogeneities may be overlooked by conventional sampling schemes. In August 2020 and for the first time, we performed continuous (once per minute) CH₄ measurements of surface water during a 584-km-long river cruise along the German Elbe to explore heterogeneities in CH₄ concentration at different spatial scales and identify CH₄ hotspots along the river. The median concentration of dissolved CH₄ in the Elbe was 112 nmol L⁻¹, ranging from 40 to 1,456 nmol L⁻¹ The highest CH₄ concentrations were recorded at known potential hotspots, such as weirs and harbors. These hotspots were also notable in terms of atmospheric CH₄ concentrations, indicating that measurements in the atmosphere above the water are useful for hotspot detection. The median atmospheric CH₄ concentration was 2,033 ppb, ranging from 1,821 to 2,796 ppb. We observed only moderate changes and fluctuations in values along the river. Tributaries did not obviously affect CH₄ concentrations in the main river. The median CH₄ emission was 251 μmol m⁻² d⁻¹, resulting in a total of 28,640 mol d⁻¹ from the entire German Elbe. Similar numbers were obtained using a conventional sampling approach, indicating that continuous measurements are not essential for a large-scale budget. However, we observed considerable lateral heterogeneity, with significantly higher concentrations near the shore only in reaches with groins. Sedimentation and organic matter mineralization in groin fields evidently increase CH₄ concentrations in the river, leading to considerable lateral heterogeneity. Thus, river morphology and structures determine the variability of dissolved CH₄ in large rivers, resulting in smooth concentrations at the beginning of the Elbe versus a strong variability in its lower parts. In conclusion, groin construction is an additional anthropogenic modification following dam building that can significantly increase GHG emissions from rivers.