Methane (CH₄) is the second most important anthropogenic greenhouse gas and reducing CH₄ emissions can lead to climate benefits on the timescale of a decade. Knowledge of the most important sources in different regions is important for designing and implementing successful mitigation strategies. We present a detailed investigation into the source mix of CH₄ emissions in Hamburg, Germany, using measurements of the CH₄ mole fraction and isotopic composition by combining data from multiple observational campaigns and an atmospheric transport model. Measurements of CH₄ isotopic composition were performed for eight months using isotope-ratio mass spectrometry (IRMS) at the Geomatikum building in the city centre, 82 m above ground level. The isotopic composition clearly demonstrates that the observed CH₄ enhancements originated mainly from microbial sources. Supporting meteorological and hydrological data provide context for explaining the temporal CH₄ variability. The highest observed CH₄ enhancements are sharp peaks from microbial sources that occur only during low tides and when air is advected from the south, where the Elbe River and the Hamburg harbour are located. Measurements with a mobile analyser along the river confirm that large emissions occur from the banks of the Elbe River during low tides. Our integrated approach demonstrates the benefit of combining detailed measurements (isotopes and mobile) and high-resolution modelling for accurately attributing greenhouse gas sources in complex environments.