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.