Methane and carbon dioxide fluxes in created and restored wetlands, and the influence of hydrology and soils on these fluxes, have not been extensively documented. Minimizing methane fluxes while maximizing productivity is a relevant goal for wetland restoration and creation projects. In this study we used replicated wetland mesocosms to investigate relationships between contrasting hydrologic and soil conditions, and methane and carbon dioxide fluxes in emergent marsh systems. Hydrologic treatments consisted of an intermittent flooding regime vs. continuously inundated conditions, and soil treatments utilized hydric vs. non-hydric soils. Diurnal patterns of methane flux were examined to shed light on the relationship between emergent macrophytes and methane emissions for comparison with vegetation–methane relationships reported from natural wetlands. Microbially available organic carbon content was significantly greater in hydric soils than non-hydric soils, despite similar organic matter contents in the contrasting soil types. Mesocosms with hydric soils exhibited the greatest rates of methane flux regardless of hydrology, but intermittent inundation of hydric soils produced significantly lower methane fluxes than continuous inundatation of hydric soils. Methane fluxes were not affected significantly by hydrologic regime in mesocosms containing non-hydric soils. There were no diurnal differences in methane flux, and carbon dioxide and methane fluxes were not significantly correlated. The highest rates of CO2 uptake occurred in the continuously inundated treatment with non-hydric soils, and there were no significant differences in nighttime respiration rates between the treatments. Implications for hydrologic design of created and restored wetlands are discussed.