In order to evaluate the soil fertility and non-point source water pollution status in representative villages of Taihu Lake watersheds rural area, 60 soil samples and 79 water samples were collected from rural area of Zhoutie and Wanshi towns, Yixing City. The nitrogen and phosphorous content of soil and water and Chemical Oxygen Demand (CODcr) of water were measured. The results demonstrated the concentrations of available nitrogen and phosphorus in vegetable fields and orchards were high, followed with wheat field, which all led to high risk of N and P loss in this area. The concentrations of available nitrogen and phosphorus in woodland were low, which led to low risk of N and P loss. Excess fertilizer application in greenhouse vegetable field, orchards and wheat field was the main reason for high fertility content in these fields. The concentrations of contaminants in river, breeding wastewater and ditch water varied significantly. The average concentrations of CODcr, ammonium nitrogen, total nitrogen and total phosphorous in river were 57, 1.7, 3.8 and 0.27 mg/L respectively. Only 10 samples in 55 samples of river water were in V level, the others were below V level.