With increases in the severity and frequency of weather extremes, there is growing concern about the ecological effects of these events. However, compared to gradual climate changes, the impacts of weather extremes have been much less studied. An extreme flood struck Poyang Lake, China, a globally important wintering ground for waterbirds, in the winter of 2015-2016. The effects of the flood on waterbird richness and abundance at Poyang Lake was assessed by comparing waterbird survey data at nine sub-lakes before (2014-2015), during (2015-2016) and after (2016-2017 and 2017-2018) the winter flood. Flooding greatly influenced waterbird abundance, with the abundance of all birds and each bird group declining by 19.7-75.5% during the flood winter relative to their values during the previous winter. Total waterbird abundance increased rapidly to pre-flood levels 1 year after the flood, suggesting that flooding mainly influenced waterbird distributions by causing waterbirds to escape to adjacent refugia. The negative impacts of extreme flooding shown here indicate that caution should be exercised in planning for a dam at the outlet of Poyang Lake. The proposed dam might have the potential to create the extreme high water levels that are unsuitable for many waterbirds.