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Quantifying source apportionments of nutrient load and their variations among seasons and hydrological years can provide useful information for watershed nutrient load reduction programs. There are large seasonal and inter-annual variations in nutrient loads and their sources in semi-arid watersheds that have a monsoon climate. The Generalized Watershed Loading Function model was used to simulate monthly nutrient loads from 2004 to 2011 in the Liu River watershed, Northern China. Model results were used to investigate nutrient load contributions from different sources, temporal variations of source apportionments and the differences in the behavior of total nitrogen (TN) and total phosphorus (TP). Examination of source apportionments for different seasons showed that point sources were the main source of TN and TP in the non-flood season, whereas contributions from diffuse sources, such as rural runoff, soil erosion, and urban areas, were much higher in the flood season. Furthermore, results for three typical hydrological years showed that the contribution ratios of nutrient loads from point sources increased as streamflow decreased, while contribution ratios from rural runoff and urban area increased as streamflow increased. Further, there were significant differences between TN and TP sources on different time scales. Our findings suggest that priority actions and management measures should be changed for different time periods and hydrological conditions, and that different strategies should be used to reduce loads of nitrogen and phosphorus effectively.