• Two surveys were conducted to estimate flood impacts on environments in estuary. • Salinity/nitrate persisted, but phosphate/chlorophyll recovered rapidly after flood. • Dam improves the dissolved oxygen condition, but the flood can enhance hypoxia. Land-ocean interaction plays an essential role in the transport fate of terrestrial matters in the coastal and shelf regions. Flood discharge from a mega river, containing massive water, sediment, and nutrient loads, could result in substantial and complex impacts on the physical and biogeochemical dynamics of coastal systems. In this study, field campaigns were conducted in a region from the Changjiang River Estuary to the East China Sea (ECS) before and after a significant flood. The impacts of the flood on physical and biogeochemical environments were assessed. The results revealed that the fluvial flood enhanced the offshore expansion of the low-salinity river plume and associated sediment/nutrient fronts. However, the area of elevated chlorophyll-a at the river mouth did not expand noticeably. A numerical model was applied to quantify the contribution of the Three Gorges Dam (TGD) to the spatial intensity and temporal duration of fluvial flood effects on estuary–shelf continuum. The results predicted a maximum of 2° latitudinal offshore displacement of the shelf water. Salinity and nitrate exhibited conservative expansions, with a longer relaxation time (~2 months) than chlorophyll-a and phosphate. After the TGD-regulated flow event ceased, salinity and nitrate effects persisted, but phosphate and chlorophyll-a recovered rapidly. The flood decreased the dissolved oxygen (DO) concentration around the river mouth and the offshore region, but not in the nearshore transient area. In contrast, the non-TGD regulation increased the regional DO concentration, which reduced the hypoxia risk. The TGD has become a crucial anthropogenic driver of environmental changes in the Changjiang Estuary-ECS continuum. [ABSTRACT FROM AUTHOR]