Chinese surface waters are severely polluted by nutrients. This study addresses three challenges in nutrient modeling for rivers in China: (1) difficulties in transferring modeling results across biophysical and administrative scales, (2) poor representation of the locations of point sources, and (3) limited incorporation of the direct discharge of manure to rivers. The objective of this study is, therefore, to quantify inputs of nitrogen (N) and phosphorus (P) to Chinese rivers from different sources at multiple scales. We developed a novel multi-scale modeling approach including a detailed, state-of-the-art representation of point sources of nutrients in rivers. The model results show that the river pollution and source attributions differ among spatial scales. Point sources accounted for 75% of the total dissolved phosphorus (TDP) inputs to rivers in China in 2012, and diffuse sources accounted for 72% of the total dissolved nitrogen (TDN) inputs. One-third of the sub-basins accounted for more than half of the pollution. Downscaling to the smallest scale (polygons) reveals that 14% and 9% of the area contribute to more than half of the calculated TDN and TDP pollution, respectively. Sources of pollution vary considerably among and within counties. Clearly, multi-scale modeling may help to develop effective policies for water pollution.