With intense anthropogenic perturbations in the Changjiang (Yangtze) River basin, the riverine loads and compositions of materials into the Changjiang Estuary have greatly changed, resulting in dramatic deterioration in the Changjiang Estuary and adjacent sea environments. Based on a long-term data set of the material loads into the Changjiang Estuary, changing trends and associated impacted factors were presented. The results showed downward trends concentrations and loads of dissolved silicate (DSi) over the past 50 years due to dam constructions in the Changjiang River. However, dissolved nitrogen (DIN) and dissolved inorganic phosphate (DIP) exhibited remarkable upward trends due to the increase of the population and the use of large-scale chemical fertilizer in the Changjiang River basin. The sharp decrease in the ratio of DSi/DIN and the increase in the ratio of DIN/DIP could cause increased Red tide bloom and decreased dissolved oxygen in the Changjiang Estuary. In addition, even though water discharge has remained almost constant, the suspended sediment discharge was shown to be sharply decreased due to the construction of dams.