Abstract: Nitrogen and phosphorus losses of surface runoff in various crop rotation systems in north of lake Erhai watershed were researched for the risk evaluation and putting countermeasures for the nonpoint pollution from agricultural source. Pollution loads of nitrogen and phosphorus were studied in four typical crop rotation systems by using the influencing factors, by analyzing the content variation dynamic of nitrogen and phosphorus in surface water of farmland and drain water in 7 townships of north lake Erhai watershed. The results show that the water soluble nitrogen is main loss of runoff water, and the contents of nitrogen have significantly contrast in farmland surface water of different crop rotation modes. The contents in ricegarlic mode are significantly higher than those of the other rotation modes, the basic trend is: RiceGarlic higher than RiceRyegrass, RiceRyegrass higher than RiceFava bean, and RiceFava bean higher than RiceRape. However, the contents of phosphorus in farmland surface water have no insignificant differences under various crop rotation modes, and the contents of phosphorus are lower. The particulate phosphorus is main loss of runoff. Generally, the contents of nitrogen and phosphorus in surface water are higher than those the ditch water, respectively. The content of total nitrogen in surface water is higher than that of ditch water (about 73% increase) in study, and the content of total phosphorus in surface water is higher than that of ditch water (about 82% increase). Fertilization in the crop growth period is one of mainly reason for the high concentrations of nitrogen and phosphorus in surface water. In this study, the loss amount of nitrogen in the RiceGarlic mode is highest, the loss amount of nitrogen under the RiceVicia faba mode is reduced by 38% compared with that of the RiceGarlic mode. So, we suggest that reasonable cropping system could be established on the basis of considering the environmental and economic benefits, and it will provide some references on readjusting cropping system and controlling nopoint pollution.