The coastal lowlands in East China are very sensitive to climate change and marine disasters, and much large-scale hydraulic engineering was recorded in the historical documents of the Late Holocene. In this study, AMS 14C and OSL were used to date three sedimentary profiles from the north and south coasts of inner Hangzhou Bay, and grain size and geochemical analyses including organic carbon, macro-elements, and alkaline earth metals were performed, while hydraulic engineering records in historical documents were compiled, in an attempt to reveal the sedimentary records of extreme climatic and hydrological events over the past 3000 years and to probe into the correlation between them and hydraulic engineering. The results show that the intensified chemical weathering during ca. 200 BCE to 900 CE in East China corresponded to the warm and humid climate during the Qin-Han and Sui-Tang dynasties. Salinity intrusion with rising local water levels occurred in the lowland plains along the south coast of Hangzhou Bay from 120 to 895 CE. Low-salinity water intrusion from 32 to 488 CE was also recorded in the stratigraphy of lowland plains along the north coast of Hangzhou Bay. The sedimentary records of the East Tiaoxi River basin show river floods about 2000 years ago. The above sedimentary records indicate that the relative sea level rose in the Hangzhou Bay area during the Qin-Han and Sui-Tang Warm Periods, resulting in frequent salinity intrusion and river floods, which coincided with the historical records of hydraulic engineering such as the construction of seawalls, river levees, and the enclosure of lakes for restoration of river floods during the Han and Tang dynasties. Such coincidence reflects that climate change profoundly affected the hydrological environment of the coastal areas in East China as well as the response of the human societies.