Large-scale hydrological alterations on land, such as river damming and river diversion, could cause reductions of silicate inputs to the sea. The Three Gorge Reservoir construction has a significant impact on silicate discharged to the sea from middle-lower reaches of the Changjiang River. The date of silicate, DIN and Si∶N ratio of Changjiang Estuary in the summers before and after the storage of the Three Gorges Reservoir were compared and analyzed to characterize their changes in the Changjiang estuary and its adjacent sea. DIN concentrations in the year 2003 and 2004 increased 1.4 and 2.3 times respectively, compared with year 1999, which has a speedup trend. Moreover, average DSi concentrations decreased from 42.12 μmol/L in 1959 to 20.98 μmol/L in 1999, decreasing 0.528 μmol/L per year in the 40 years before river storage of the Three Gorges Reservoir. By 2003, DSi concentration decreased to 18.86 μmol/L, average decreasing 0.53 μmol/L per year during 1999 to 2003, which seemed as before. But, after the storage, it decreased to 15.9 μmol/L in 2004, decreasing 2.95 μmol/L in one year. Meanwhile, the sediment discharge to the estuary was also decreasing. The river damming mainly caused this drastic decrease. In addition, the decrease trend of DSi effective concentration in the river end of the estuary also demonstrated that the storage affected DSi discharge flux to the sea. The average values of Si∶N ratio decreased from 1.66 in 1999 to 1.09 in 2003, and to 0.42 in 2004 with a large area of the estuary lower than 1. The sharp decrease of Si∶N ratio was in 1960s and 1970s and decreased to 2 in 1980s as same time, N/P ratio raised from 2 to 12. The extensive changes of Si∶N and N∶P could make severe impacts on the structure of the Changjiang estuarine ecosystem. It is a pity that we did not make any assessment for that in detail until now. By contrast, there was remarkable correlation between DSi decreasing and the changes of sediment discharge of the Changjiang. However, the rising concentration of DIN is due to the excessive utilization of fertilizer along the middle-lower reaches. There have been tendencies for nutrient structure imbalance, which may lead the ecosystem changes in the Changjiang estuary, including alga blooms of diatoms pre-reservoir becoming enriched in flagellates. All of these changes might be directly related to human activities.