Nonpoint source pollution generated by agricultural production and city construction has been studied for decades, but very few researches have been conducted on the regional assessment of nonpoint source pollution in the acid rain regions, particularly relating to the control of pollutant in the drinking water source areas. In this study, an integrated framework was applied to estimate nitrogen and phosphorous load in a typical acid rain influenced reservoir, China. The method comprised three separate steps: (1) a watershed model—soil and water assessment tools—was used to estimate nitrogen and phosphorous load from the upper stream watershed; (2) collection of acid rain samples, together with a GIS-based calculation to estimate the atmospheric deposition flux; (3) introduction of a simple export coefficient method. The case study indicated atmospheric deposition accounted for 56.75 % of total nitrogen load during the year, with the highest level of deposition load taking place during the wet season. Maximum phosphorous (93.37 %) was linked to the upstream runoff, originating from the upper watershed. Further analysis by watershed model and export coefficient method indicated forest exported most total nitrogen (27.72 %) and total phosphorous (58.78 %) in the upstream watershed. Results indicated that in the region influenced by acid rain, the nitrogen management should encompass the management of land use practices and the control of acid rain in catchments feeding into drinking water storage areas. It could be inferred that NOX emissions might cause both globe warming and eutrophication in the drinking water sources. This paper could provide a basis for water quality management in such regions.