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Exploring the responsibility subject of water pollution is the foundation of ecological environmental control and protection. A water pollution sources apportionment and contribution rates analysis method based on one-dimensional model was developed. It was adopted in a typical trans-boundary river section in the sub-watershed of the Yangtze River Basin. The contribution rates of different time period and distinctive administrative regions of the section were calculated. Results show that urban living point sources contributed most to chemical oxygen demand (COD) and ammonia nitrogen (NH4±-N) followed by rural living sources. Agricultural sources are the main pollution source of total phosphorus (TP) throughout the year. Almost seven township regions in Deyang City, especially the Bajiaojing community and Xinshi Town, should be mainly responsible for water pollution. However, in different month and water periods, contribution rates change along with the precipitation variability. Sewage treatment plants and industrial enterprises contributed the most to pollutants in the dry season, but the living sources and non-point agricultural sources have bigger contribution rates in the wet season. There is a strong negative correlation between precipitation and contribution rate. Methods adopted in this paper can be used to analyze the pollution sources in the refined management of the water environment, so as to trace the main body of environmental responsibility.