Analyses of sedimentary evidence in the form of spores, pollen, freshwater algae, dinoflagellate cysts, phytoliths and charcoal from AMS 14C-dated, Holocene-aged sequences provide an excellent opportunity to examine the responses of Neolithic agriculturalists in the lower Yangtze to changing environments. Evidence from two sites close to the southern margin of the Yangtze delta and separated by what is now Hangzhou Bay attests the critical importance to early attempts at food production of access to freshwater resources. More readily, if episodically, available freshwater resources during the early to mid-Holocene on the Hangjiahu plain may have encouraged an early reliance on rice-based agriculture, which in turn facilitated the accumulation of agricultural surpluses and cultural diversification. Cultural change was relatively attenuated and human population pressures possibly lower on the Ningshao plain, seemingly because of much more profound environmental impacts of variations in local hydrological conditions, and because predominantly saline conditions, associated with rising relative sea level, hampered the early development of irrigated agriculture. The evidence, although largely dating to the early and middle parts of the Holocene, provides a timely warning of the complexity of vulnerability to climate change-induced processes of agriculture, and indeed human activities more generally, on megadeltas in Asia.