Remote sensing can help to derive turbulent fluxes in the atmosphere even if the remote sensing technique used itself is not able to resolve turbulent fluctuations. Turbulent fluxes are important components of atmospheric energy and substance budgets and they play a dominant role in the surface-atmosphere exchange. Apart from high-resolution in situ measurements it is difficult to determine them. This paper presents an inverse method to derive a regionally-averaged vertical turbulent flux of methane from the surface into the atmospheric boundary layer. The determination of aggregated surface emission fluxes of methane from an agricultural area in Southern Germany on an intermediate scale between the local and the regional scale is based on using a boundary layer budget method combined with surface-based acoustic remote sensing of the mixing-layer height with a sodar. The order of magnitude of the resulting methane emission fluxes coincide well with the national methane emission inventory.