The Clarence River estuary experienced extensive oxygen depletion and fish kills following overbank flooding in 2001. This paper examines the chemical composition and volume of surface water draining from two floodplain sulfidic backswamps into the Clarence River estuary after the flooding. Water draining from the backswamps was severely deoxygenated (<5 μmol L-1 O2), developed high chemical oxygen demand (∼5000 μmol L -1) and became enriched in iron (∼350 μmol L-1) during the weeks following the flood. The chemistry of this anoxic drainage water was influenced by anaerobic decomposition of backswamp vegetation, iron and sulfur biogeochemistry in backswamp surface sediments and shallow ground water input from acid sulfate soils. This study shows that artificial drainage of sulfidic backswamps increased the volume of anoxic surface water with high deoxygenation potential exported to the estuary, increasing the severity and duration of estuarine oxygen depletion in the latter stages (>6 days post-peak) of flood recession. In the absence of artificial drainage, most of the floodwaters with high deoxygenation potential would have been retained in the landscape and not exported to the estuary as observed during this flood.