Processes driving production and transport of CH₄ in wetlands are complex. We present an algorithm to separate open-water automatic chamber CH₄ fluxes into diffusion and ebullition. This helps to reveal dynamics, identify drivers and obtain reliable CH₄ emissions. The algorithm is based on sudden concentration changes during single measurements. A variable filter is applied using a multiple of the interquartile range. The algorithm was verified for data of a rewetted former fen grassland site.