We investigated the effect of the Three Gorges Project and other dams on the load of phosphorus (P) to the middle and lower Yangtze River (MLY) and discussed the alteration of P on the ecosystem of the MLY. We collected data for continuous flow and sediment over the past 60 years and observed the concentrations of total P (TP) and particulate P (PP) in the pool reaches of the Three Gorges Reservoir (TGR), both before and after the impoundment in 2003. As a result, we obtained highly positive correlations between P and sediment and revealed two changes that were caused by the impoundments: (1) the sediment load to the MLY decreases by 91% and the river becomes almost clear; and (2) the loads of TP and PP to the MLY are sequestered by 77% and 83.5% annually and 75% and 92% in dry seasons, respectively. Because P was the limiting nutrient for bioactivity in the MLY before 2003, such significant reductions, along with the many other consequences of the dams, will not only further reduce the bioavailability of P but also increase the existing high ratio of nitrogen (N) to P. Therefore, it is quite possible to alter the nutrient regime and reduce the aquatic primary productivity of the MLY. Given that many large dams with huge reservoirs are under construction or planned upstream and elsewhere, studies focused on the long-term effects of sediment and P reduction deserve a high priority for the protection of lowland rivers and aquatic ecosystems.