Floods frequently produce deoxygenation and acidification in waters of artificially drained coastal acid sulfate soil (CASS) wetlands. These conditions are ideal for carbon dioxide and methane production. We investigated CO₂ and CH₄ dynamics and quantified carbon loss within an artificially drained CASS wetland during and after a flood. We separated the system into wetland soils (inundated soil during flood and exposed soil during post flood period), drain water, and creek water and performed measurements of free CO₂ ([CO₂*]), CH₄, dissolved inorganic and organic carbon (DIC and DOC), stable carbon isotopes, and radon (²²²Rn: natural tracer for groundwater discharge) to determine aquatic carbon loss pathways. [CO2*] and CH₄ values in the creek reached 721 and 81 μM, respectively, 2 weeks following a flood during a severe deoxygenation phase (dissolved oxygen ~ 0% saturation). CO₂ and CH₄ emissions from the floodplain to the atmosphere were 17-fold and 170-fold higher during the flooded period compared to the post-flood period, respectively. CO₂ emissions accounted for about 90% of total floodplain mass carbon losses during both the flooded and post-flood periods. Assuming a 20 and 100 year global warming potential (GWP) for CH₄ of 105 and 27 CO₂-equivalents, CH₄ emission contributed to 85% and 60% of total floodplain CO₂-equivalent emissions, respectively. Stable carbon isotopes (δ¹³C in dissolved CO₂ and CH₄) and ²²²Rn indicated that carbon dynamics within the creek were more likely driven by drainage of surface floodwaters from the CASS wetland rather than groundwater seepage. This study demonstrated that >90% of CO₂ and CH₄ emissions from the wetland system occurred during the flood period and that the inundated wetland was responsible for ~95% of CO₂-equivalent emissions over the floodplain.