Soil and water loss has been effectively controlled by the comprehensive treatment of soil and water conservation in the hilly regions of south China, but the problem of non-point source pollution still exists. It is very important to study the spatial distribution of non-point source pollution in watersheds for the treatment of this kind of pollution. Taking the Songxi River Watershed as the representative of the hilly regions in south China, based on the field investigation, three representative land use types in watershed were selected as the sampling points, including the ponds within the catchment area, the downstream of Songxi River and the watershed outlet. The effects of different land use types on the spatial distribution of total nitrogen (TN), ammonium nitrogen (NH+4—N), nitrate nitrogen (NO-3—N) and total phosphorus (TP) were analyzed using water samples collected from June to November in 2016. The results showed that the total nitrogen was the main pollutant, and its concentration at the sampling point of the watershed outlet was the highest, ranging from 0.9 to 3.15 mg/L. Residential area and farmland contributed the highest to the pollution of small watersheds. Because the social and economic activities are frequent due to the fast economic development in these areas, but the infrastructure construction is relatively lagging behind. The spatial distribution characteristics of nitrate nitrogen concentration and total nitrogen concentration were consistent, and the time variation trend of nitrate nitrogen, ammonium nitrogen and total nitrogen was the same. It is found that nitrogen pollution in watershed is significantly affected by rainfall, and phosphorus pollution is affected by fertilization habits.