Wetlands are the most important natural source of methane (CH4) to the atmosphere, and there is still considerable uncertainty of CH4 flux and net carbon budgets of wetlands. This uncertainty is due in part to the complex role of wetland vegetation in controlling methane production, oxidation and transport, which challenge the modeling and forecast of CH4 fluxes. We combined CH4 and carbon dioxide (CO2) fluxes measured by the eddy covariance technique during two consecutive growing seasons with continuous measurements of water levels and water temperature in a Typha angustifolia L patch of a temperate wetland. We seek to evaluate the role of vegetation in CH4 flux processes. To this end, we determined the relationship between CH4 and CO2 fluxes, directly and indirectly linked to plant activity. Our results indicated significant but opposing relationships between CH4 and CO2 fluxes during the daytime and nighttime. Consequently, when analyzed on a diel timescale, this relationship was not significant. Both CH4 and CO2 fluxes were highly dependent on environmental drivers, and thus, the correlations observed at both the nighttime and daytime were likely the result of a shared response to environmental variables. Focusing on water temperature (the most commonly observed environmental variable in wetlands) and water level (the most commonly controlled one) as operational control variables for wetlands, we identified “hot” condition combinations when CH4 flux and net ecosystem CO2 uptake are maximized at half hourly and diel scales.