The purposes of this study were to suggest the methodology to select prior areas in the environmental pollution survey for livestock excreta (EPSLE) as well as to elucidate the validity of the methodology. In this study, the prior areas in the EPSLE were determined by examining the number of compost facilities categorized according to the three levels of size including the basin, the sub-basin and the watershed, respectively, based on the data from “Annual Nation-wide Pollution Sources Survey (2012)”. The results suggested that the list of prior basins were Nakdong, Geum, Youngsan and Han river basins in order. Also, it was examined that the prior sub-basins in the four river basins including Nakdong, Geum, Youngsan and Han rivers were Naesung Stream, Geumgang Gongju, Juam Dam and Namhan Downstream, respectively. The prior watersheds in the sub-basins of Naesung stream, Geumgang Gongju, Juam Dam and Namhan Downstream were Seocheon Downstream, Geum Stream, Gyeombaek Suwipyo and Yanghwa Stream, respectively. The validity of the methodology used in this study was elucidated by analyzing the correlation of the number of compost facilities with the concentrations of T-N and T-P observed in the end-points of sub-basins. The results of correlation analysis showed that the concentrations of T-N and T-P increased with the number of compost facilities. Specifically, there was the stronger correlation between the number of compost facilities and the concentrations of T-N than that for T-P. Consequently, it was proved that the methodology used in this work was valid and rational for the selection of prior areas in environmental pollution survey for EPSLE.