We measured CO2 and CH4 fluxes for 6 years following permanent flooding of an agriculturally managed organic soil at two water depths (~25 and ~55 cm standing water) in the Sacramento–San Joaquin Delta, California, as part of research studying C dynamics in re-established wetlands. Flooding rapidly reduced gaseous C losses, and radiocarbon data showed that this, in part, was due to reduced oxidation of "old" C preserved in the organic soils. Both CO2 and CH4 emissions from the water surface increased during the first few growing seasons, concomitant with emergent marsh establishment, and thereafter appeared to stabilize according to plant communities. Areas of emergent marsh vegetation in the shallower wetland had greater net CO2 influx (-485 mg Cm-1 h-1), and lower CH4 emissions (11.5 mg Cm-2 h-1), than in the deeper wetland (-381 and 14.1 mg Cm-2 h-1, respectively). Areas with submerged and floating vegetation in the deeper wetland had CH4 emissions similar to emergent vegetation (11.9 and 12.6 mg Cm-2 h-1, respectively), despite lower net CO2 influx (-102 gC m-2 h-1). Measurements of plant moderated net CO2 influx and CH4 efflux indicated greatest potential reduction of greenhouse gases in the more shallowly flooded wetland.
