The lower Yangtze is one of the regions of origin of rice agriculture but it is unclear if environmental change drove the transition from hunting-gathering to agriculture. Long-term and continuous lacustrine records of anthropogenic fire are a more effective means of addressing this problem than the fragmentary terrestrial records available for the lower Yangtze region. We constructed a Holocene fire history revealed by records of black carbon content (BCC) and grain size of the sediments of Lake Nanyi in the lower Yangtze. Our results show the following: 1) Peaks in fire activity occurred during ∼8400–6500 (fire peak P1) and ∼ 1100–0 cal BP (fire peak P2), while weaker fire activity occurred during ∼6500–1100 cal BP (S2). 2) This temporal pattern of fire activity, with a double peak (P1-S2-P2), was asynchronous from east to west across the lower Yangtze. The warm and humid climate would not have caused intense fires and the reduction of forest during ∼8400–6500 and ∼ 1100–0 cal BP. Therefore, we suggest that anthropogenic ignitions, corresponding to pronounced population fluctuations after 8400 cal BP, dominated the regional fire activity. Combined with archaeological evidence, the inverse relationship between the agricultural and population levels and fire intensity during the mid-Holocene suggests that fire intensity at this time was the result of the diversity of landscape types associated with prehistoric subsistence patterns, rather than the magnitude of anthropogenic activity. Combined with sea level, rainfall and archaeological evidence, we propose a mechanism whereby asynchronous water-level rise during ∼8400–6500 cal BP forced the migration of humans to the foothills where they often used fire to modify the landscape as part of a broad-spectrum subsistence pattern. Whereas, water-level fall after 6500 cal BP expanded the area of open ground for human settlement, and in this less diverse landscape, less use was made of fire in agricultural subsistence. Overall, our study reveals how regional water-level, driven by sea-level rise and extreme rainfall, delayed the transition from hunting-gathering to agriculture in the lower Yangtze region.