The temporal-spatial distribution of Neolithic sites shows a long period of absence of human settlements during the early Holocene on the Yangtze Delta, and the area has not been colonized until 7000 aBP, corresponding to the onset of the Majiabang culture. Besides the regions east to the sandbar of Maqiao Site in Shanghai, foraminifera are not found in Neolithic cultural layers since 7000 aBP, indicating a widespread transgression between 10000 and 7000 aBP. Evidence of radiocarbon-dated cultural relics, foraminifera and pollen records from the Hemudu Site suggests that the Hemudu culture emerged and developed during the mid-Holocene Climatic Optimum. Therefore, the hypothesis of a mid-Holocene sea-level highstand along the Yangtze Delta and Ningshao Plain from 7000 to 5000 aBP is an open debate. New evidence from archaeological excavations and bio-stratigraphy suggests that, prior to 7000 aBP, a high sea level occurred along the Ningshao Plain. Subsequently, the sea level was lowered between 7000 and 5000 aBP, and the area suffered from frequent floods from 5000 to 3900 aBP.