To reduce the harmful effects of irrigated agriculture on the environment, the evaluation of alternative irrigation water management practices is essential. The contents of total-phosphorus, nitrate nitrogen, and ammonium nitrogen in rural aquatic bodies typical of the Taihu Lake region (Yixing, Wangzhuang, and Xinzhuang) were determined during 2 years. The results showed that the concentrations of nitrogen and phosphorus during the rainy season were higher than in other months. The concentration of ammonium nitrogen in farmland drainage was higher than that of nitrate nitrogen. Ammonium nitrogen and nitrate nitrogen were the main pollution sources in rural groundwater. However, the pollution by ammonium nitrogen was worse than nitrate nitrogen. The annual average values of ammonium nitrogen in Yixing and Wangzhuang were 1.596 and 2.103 mg L(-1); with maximum values of 5.782 and 5.441 mg L(-1), respectively, exceeding the lower limit for type V water quality by a factor of 10. Concentrations of nitrate nitrogen in groundwater in Xinzhuang from May to September exceeded the limit value (10 mg L(-1)) for drinking water prescribed by the World Health Organization. Therefore, this groundwater was not suitable to drink. In Taihu Lake, the average concentration of phosphorus over 2 years was 0.492 mg L(-1) and pollution by phosphorus in Taihu Lake was worse than other farmland drainage because of the trend of total-phosphorus accumulation. In addition, the average concentrations of nitrate nitrogen and ammonium nitrogen in Taihu Lake were 2.152 and 2.885 mg L(-1), respectively over 2 years, indicating that the water in the Taihu Lake is constantly in danger of eutrophication. Because of the transformation of ammonium nitrogen to nitrate nitrogen, there was a connection between the concentrations of ammonium nitrogen in farmland drainage and nitrate nitrogen in groundwater. There was also a significant positive linear correlation between the concentrations of ammonium nitrogen in farmland drainage and in shallow groundwater.