Soils contain nearly three times the amount of carbon (C) than the atmosphere, with C turnover times ranging from centuries to millennia. Although wetland soils represent a relatively small portion of the terrestrial landscape, they account for an estimated 20-30% of the global C reservoir. Seasonally flooded soils are likely the most vulnerable wetlands to climate change, as changing temperature and precipitation patterns are expected to alter the timing and duration of flooding. Seasonal variations in soil moisture are recognized as a critical control on soil C stocks and CO2emissions. However, the relative influence of associated changes in soil oxygen availability, root dynamics and the stability of mineral-organic associations are largely unknown. The overarching goal of this study was to examine the relative influence of redox state, root density and mineralogy on C cycling within seasonally flooded soil. To accomplish this goal, we combined seasonal monitoring of soil moisture, redox potential, and carbon dioxide emissions with a characterization of organic matter composition, mineralogy and root biomass along upland to lowland transects. We found that water saturation was the limiting factor for CO2emissions from seasonal flooded lowland soils, whereas soil temperature primarily regulated emissions from upland soils. Seasonal water saturation also resulted in topsoil C accumulation in lowlands compared to uplands, despite experiencing prolonged aerobic periods. Moreover, the C that accumulated in lowland topsoils was more chemically reduced compared to upland soils. However, the C chemistry in the subsoil showed the opposite trend of being more reduced in uplands compared to lowland subsoils. In sum, our results suggest that anaerobically protected soil C in seasonal flooded soils is particularly vulnerable to changing moisture regimes in response to climate change. To what extent this expected C loss is compensated by upland plant encroachment, or the neoformation of mineral-organic associations, warrants future research.