Net ecosystem carbon dioxide (FCO2) and methane (FCH4) exchanges were measured by using the eddy covariance method to quantify the atmospheric carbon budget at a Typha- and Nymphaea-dominated freshwater marsh (March 2011 to March 2013) and a soybean cropland (May 2011 to May 2012) in northwestern Ohio, USA. Two year average annual FCH4 (49.7 g C-CH4 m−2 yr−1) from the marsh was high and compatible with its net annual CO2 uptake (FCO2: −21.0 g C-CO2 m−2 yr−1). In contrast, FCH4 was small (2.3 g C-CH4 m−2 yr−1) and accounted for a minor portion of the atmospheric carbon budget (FCO2: −151.8 g C-CO2 m−2 yr−1) at the cropland. At the seasonal scale, soil temperature associated with methane (CH4) production provided the dominant regulator of FCH4 at the marsh (R2 = 0.86). At the diurnal scale, plant-modulated gas flow was the major pathway for CH4 outgassing in the growing season at the marsh. Diffusion and ebullition became the major pathways in the nongrowing season and were regulated by friction velocity. Our findings highlight the importance of freshwater marshes for their efficiency in turning over and releasing newly fixed carbon as CH4. Despite marshes accounting for only ~4% of area in the agriculture-dominated landscape, their high FCH4 should be carefully addressed in the regional carbon budget.