The eddy covariance technique was employed with a tunable diode laser spectrometer to quantify methane flux from a prairie marsh dominated by Phragmites australis in north‐central Nebraska, USA. The observations spanned the entire growing season (April to October) and a wide range of weather conditions, allowing a quantitative assessment of the physical and biological controls of methane emission in this ecosystem. Diel patterns in methane emission varied markedly depending on plant growth stage. Prior to plant emergence above water, the rate of methane emission from the marsh was fairly constant throughout the day. After emergence above water, there was a gradual increase in methane emission after sunrise with a peak in late afternoon. Significant changes in diel patterns were observed after tillering. Then, the diel pattern was characterized by a mid‐ to late‐morning peak and a 2‐to 4‐fold increase in methane emissions from night to daytime. In early stages of plant growth, molecular diffusion through dead/live plants and the standing water column seemed to be the primary transport mechanism. After tillering, a transition occurred in the transport mechanism from a molecular diffusion to a convective throughflow, which is a rapid and active gas transport driven by pressure differences. The role of convective throughflow became less important as the plants senesced. Integrated methane emission over the six‐month measurement period (April–October) was about 64 g CH4 m–2. On an annual basis, we estimate the annual methane emission from this ecosystem to be ≈ 80 g CH4 m–2 and that about 80% of the total methane emission occurred between late April and late October.