The seasonal characters of the water flux and suspended substance, phosphorus in the water of input rivers of Three Gorges Reservoir (TGR) were discussed, and the their distributions among three major input rivers (Changjiang river, Jialingjiang river and Wujiang river) were studied, according to the survey conducted from Jan. 2004 to Dec. 2005. The results indicate that those parameters' seasonal changes are obvious. The flux and suspended substance in abundant water period are more higher than them in low water period, which displays suspended substance origins from bedload and that the water and soil severely lose in drainage areas of three input rivers. In the three monitor sections of input rivers of TGR, the average contents per year of total phosphorus are about 0.12-0.29 mg/L, which exceeds the 1970s level of the three input rivers. Most of total phosphate is total solid phosphate (TPP) exceeding 75% of them. TP and TPP have both distinct positive correlation with the flux and suspended substance in water of input rivers of TGR, and TPP and TP have also the same correlation, which means that phosphate pollution in the input rivers of TGR comes from bedload. The nonpoint source pollution has had far-reaching influence upon phosphate pollution. Nitrogen and phosphate are not the major limiting factor of the nutritious salts in the input rivers of TGR. The rate of between nitrogen and phosphate (N/P) is in higher level (above 30), that is phosphate first will reach lower level and maybe become the limiting factor of the nutritious salts in the input rivers of TGR.