In order to improve water quality of upper watershed of Paldang reservoir, it is necessary to evaluate non-point source pollution loads and identify critical watershed pollution sources. A GIS based Soil and Water Assessment Tool was applied to evaluate model application and reliability, estimate NPS pollution load, identify critical watershed by NPS pollution sources, and suggest various best management practices for Kyongan Stream watershed. Yearly NPS pollution loads were estimated 30.0% SS, 60.1% TN and 35.4% TP, respectably. The watershed pollution load is mainly decided by precipitation condition and SS and nutrients load have a significant regression relationship. Based on 10-year average yearly NPS pollution load, critical sub-watersheds were identified. The No. 5 and 17 which have lots of relatively intensive agricultural fields and scattered industrial area were vary critical sub-watersheds and under more intensive pollution load. In order to control critical watershed, watershed best management practices such as scientific fertilizer, contour farming and parallel terrace, transferring the sloppy farmland to grass or forest and constructing a buffer zone, and constructing wetlands and retention ponds will be applied. Overall the SWAT model can be efficiently used for identification of critical sub-watersheds in order to develop a priority watershed management plan to reduce water pollutions.