The surface of the lowland deltaic plain around Taihu (Lake Tai), south of the Yangtze river mouth in eastern China, lies near sea level and until recent drainage and development by human societies was mostly covered by wetlands of various types. It was created by regular overbank flooding, mainly from the Yangtze, and the deposition of mostly mineral sediments over the several millennia since sea level regained its current altitude in the early mid-Holocene and progradation of the Yangtze delta began. Fluvial activity has therefore been the dominant influence on sedimentation in the Taihu lowlands, and in the lower Yangtze valley generally, and has determined the character of the mainly inorganic sediment sequences that have accumulated there, with autochthonous deposition of organic sediments within the local wetland plant communities playing a minor role. The presence of both clastic flood horizons and peat layers within the deposits of the Taihu plain attests to great variability in the magnitude of fluvial input from the Yangtze, with repeated extreme floods occurring at some periods, but with periods when the growth of peat layers shows low water tables, little exogenic sediment input and so little fluvial influence. We have examined the published evidence for these different depositional environments in the lower Yangtze and the Taihu plain during the Holocene, comparing the flood history with the middle and upper reaches of the Yangtze catchment. Discrete phases of high or low flooding influence are recognised, and these correspond with large-scale Holocene climate history. Intensified human land use in recent millennia has complicated this relationship, amplifying the flooding signal. Our palynological research shows that algal microfossil type and abundance is a useful proxy for changing water depth and quality in the aquatic environments of the Holocene Taihu wetlands, and can recognise flooding events that are not registered in the floodplain lithological sequences.