Ponds, rivers and reservoirs are the basic elements of water environment in a rural watershed, especially in the humid regions of Southeastern China. The water quality model for Lita-chenzhuang rural watershed in Mountain Mao Region is developed based on the WASP model. It is a combination among field investigation, GIS spatial analysis, pollution loads estimation and so on. The result shows that the order of contamination level of the main water quality indicators are total nitrogen (TN), total phosphorus (TP), permanganate index, and ammonia nitrogen, respectively. For TN concentrations of the year, 52%-100% of different water bodies are worse than GradeⅤ of Environmental Quality Standards for Surface Water of China(GB 3838-2002), while the ponds are relatively close to the rivers on the contamination. During summer and winter, 2%-6% of rivers and 8%-14% of ponds have exceeded the upper bound of GradeⅤ in TP concentrations.Ponds in the center of the watershed and near the village are obviously more contaminated. The pollution loads are the main uncertainty factor of the water quality model. So the refinement on planting patterns could improve the simulation results on the whole. The pollutants from unfenced livestock and poultry have more effect on the ponds, while the water quality of the rivers is more vulnerable to sewage and garbage. This study establishes the links of water quality in different water bodies, which are affected by non-point source pollution in a typical rural watershed. It is also useful to formulate mitigation measures on rural water environment.