The objective of this study was to investigate non-point sources (NPS) pollution and prioritize management areas affected by NPS pollution in the Saemangeum Watershed. AHP (Analytical Hierarchy Process) technique was selected to prioritize sub-watersheds for effectively managing NPS pollution in this study areas. Generation properties of NPS pollution, discharge properties of NPS pollution, and runoff properties of NPS pollution were selected and set for AHP. Weighted descriptors including indicators like numbers of livestock, land- and livestock-system loads, rainfall, and impervious area ratio were generalized from 0 to 1 and multiply each index based on screened 17 survey data. The results were visualized as maps which enable resource managers to identify sub-watersheds for effective improving water quality. The sub-watersheds located in Gongdeok-Myeon, Yongji-Myeon, Hwangsan-Myeon of Gimje-Si were selected for managing NPS pollution control areas. This result presented that these sub-watershed are more affected by the pollution from livestock-system than from land-system. The finding from this study can be used to screen sub-watersheds that need further assessment by managers and decision-makers within the study area.