To tackle the problem of water eutrophication of the Nansi Lake along the eastern line of the South-North Water Diversion Project in China, field experiments were carried out on fertilization in farmland under wheat-maize rotation, typical of the region, to explore its effect of controlling S and P loss. In the experiments, market–available fertilizers were used and in-situ lysimeters and surface runoff pools were set up to collect leachate and runoff for lab analysis. Results show that fertilization, regardless of its method, reduced nitrogen and phosphorus loss with water in both crop seasons. The effect varied with fertilization method. NO3--N was the main form of nitrogen lost with runoff water, accounting for 82.7%~86.4% in the maize season and for 94.2% 96.5% in the wheat season, however, it declined slightly in leachate, which suggests that surface runoff is the main route of nitrogen loss. Nitrogen loss during the maize season amounted to 67.0%~71.4% of the total of a year. P loss via surface runoff consisted almost equally of dissolved phosphorus and particulate phosphorus, while P loss via leaching was dominated with dissolved phosphorus, and accounted for a larger proportion of the total. A greater proportion, 54.4% ~ 63.1% of the P loss of a year occurred during the maize growing season. Taking into account both control of N and P loss and crop production of a year, it is advisable to apply decrement controlled-release nitrogen fertilizer or optimize fertilization coupled with straw incorporation for maize season, and optimize fertilization or apply decrement controlled-release nitrogen fertilizer for wheat.