This paper takes Zhexi hydraulic region in Taihu Basin as the study area. Using hydraulic analysis function of Arcgis8.3, the drainages were delineated by selecting the monitoring points and discharge stations as outlets. The landuse map was finished by denoting the TM/ETM image. The precipitation map was finished by spatial interpolation using the rainfall monitoring records. Overlaying the drainage boundary, landuse map and precipitation map, the rainfall, areas of different landuse types, and runoff pollution concentration and runoff were calculated. Based on these data in different drainages, by Origion7.0 regression tool, an equation is found to predict runoff using the relationship between runoff, precipitation depth and percentage of land use in each of the drainages. Selecting the sub-watershed which is mainly composed of forest landuse type, the mean runoff concentration (MRC) from sub-watershed has been estimated. The mean runoff concentration of farmland has been estimated by the same methods after removing the contribution of forest landuse type. The result is: for the forest landuse type, the mean runoff concentrations of COD, BOD, Total N and Total P are 2.95 mg/l, 1.080 mg/l, 0.715 mg/l, and 0.039 mg/l; for the farmland, the mean runoff concentrations of COD, BOD, Total N and Total P are 5.721 mg/l, 3.097 mg/l 2.092 mg/l, and 0.166 mg/l. Using these results, the agricultural non-point pollution loads have been assessed. The loads of COD, BOD, Total N and Total P in Zhexi region are 14631.69 t/a, 6401.93 t/a, 4281.753 t/a and 287.67 t/a respectively.