In this study, the characteristics of nonpoint pollutant outflow and contribution rate of pollution in Songya-stream mainstream and tributaries were analyzed. Further, water pollution management and improvement measures for pollution-oriented rivers were proposed. An on-site investigation was conducted to determine the inflow of major pollutants into the basin, and it was found that pollutants generated from agricultural land and livestock facilities flowed into the river, resulting in a high concentration of turbid water. Based on the analysis results of the pollution load data calculated through actual measurement monitoring (flow and water quality) and the occurrence and emission load data calculated using the national pollution source survey data, the S3 and S6 were selected as the concerned pollution tributaries in the Songya-stream basin. Results of cluster analysis using Pearson correlation coefficient evaluation and Density based spatial clustering of applications with noise (DBSCAN) technique showed that the S3 and S6 were most consistent with the C2 cluster (a cluster of Songya-stream mainstream owned area) corresponding to the mainstream of Songya-stream. The analysis results of the major pollutants in the concerned pollution tributaries showed that livestock and land pollutants were the major pollutants. Consequently, optimal management techniques such as fertilizer management, water gate management in paddy, vegetated filter strip and livestock manure public treatment were proposed to reduce livestock and land pollutants.