Abstract. Processes driving the production, transformation and transport of methane (CH₄) in wetland ecosystems are highly complex. We present a simple calculation algorithm to separate open-water CH₄ fluxes measured with automatic chambers into diffusion- and ebullition-derived components. This helps to reveal underlying dynamics, to identify potential environmental drivers and, thus, to calculate reliable CH₄ emission estimates. The flux separation is based on identification of ebullition-related sudden concentration changes during single measurements. Therefore, a variable ebullition filter is applied, using the lower and upper quartile and the interquartile range (IQR). Automation of data processing is achieved by using an established R script, adjusted for the purpose of CH₄ flux calculation. The algorithm was validated by performing a laboratory experiment and tested using flux measurement data (July to September 2013) from a former fen grassland site, which converted into a shallow lake as a result of rewetting. Ebullition and diffusion contributed equally (46 and 55 %) to total CH₄ emissions, which is comparable to ratios given in the literature. Moreover, the separation algorithm revealed a concealed shift in the diurnal trend of diffusive fluxes throughout the measurement period. The water temperature gradient was identified as one of the major drivers of diffusive CH₄ emissions, whereas no significant driver was found in the case of erratic CH₄ ebullition events.