Non-point source pollution (NPSP) is a major challenge for current global water resources. The output characteristics of pollutants under different land use types are very important for controlling NPSP. In this study, long-term positioning monitoring and an analysis of rainfall runoff from different land use types were used to evaluate a typical watershed in the water source area of the middle route of the South-to-North Water Diversion Project (MR-SNWDP). The results show significant differences in nitrogen and phosphorus content in the runoff water bodies of various land use types. The nitrogen and phosphorus content in the MR-SNWDP was directly related to rainfall intensity and the fertilization period in the runoff following fertilization of farmland and vegetable plots. This nitrogen and phosphorus content was also observed to be significantly higher in the fertilization period than in other periods. The loss of nitrogen and phosphorus in forestland was greatly affected by rainfall intensity. Nitrogen in runoff comes primarily from farmland and vegetable fields, where its main form is nitrate nitrogen (NN). Vegetable fields are the main source of phosphorus, where its primary form is soluble phosphate (PO43&minus / -P). Nitrogen and phosphorus have a defined incubation period during the dry season. Farmland and vegetable fields receive less rainfall during the dry season and it is difficult to form effective runoff / this allows nitrogen and phosphorus deposition. The runoff formed by the first rainfall at the beginning of the flood season (April or May) will carry a large amount of nitrogen and phosphorus from the soil into water bodies. Therefore, it is crucial to pay careful attention to the season when attempting to control NPSP.