Abstract: The external pollutant loading model and the nitrogen and phosphorus fluxes model, combining land use pattern and meteorological data, were used to established an empirical model of nitrogen and phosphorus loading in four river watersheds of Yan’an City, for analyzing the response relation of the fluxes of nitrogen and phosphorus on net anthropogenic nitrogen and phosphorus input, precipitation, land use pattern and other factors. According to the results, the net anthropogenic nitrogen and phosphorus input, precipitation and land use pattern were the main causes for the change of the nitrogen and phosphorus fluxes. Precipitation could respectively explain 25.67% and 18.29% of the nitrogen and phosphorus fluxes variation, and the increasing precipitation will significantly increase the nitrogen and phosphorus fluxes. A meteorological dataset from regional climate models was used to simulate the short-term and long-term variation of nitrogen and phosphorus fluxes under different development scenarios, and the results showed that driven by the change of climate, even if the net anthropogenic nitrogen and phosphorus loading and the land use pattern remained unchanged, the future nitrogen and phosphorus fluxes would still increase in the long-term prediction. The increasing of forest land could mitigate a certain extent of the influence of precipitation on nitrogen and phosphorus fluxes. These results indicated that climate change as well as anthropogenic activities could affect the nitrogen and phosphorus fluxes, and the impact of climate change on the effectiveness of nitrogen and phosphorus reduction programs should be considered while formulating the nitrogen and phosphorus reduction programs.