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Objective A prerequisite for managing a catchment is to comprehensively understand the changes in its water quality. Using different methods, this paper comparatively analyzes the spatiotemporal variation in water quality of the Yangtze River, including its main streams and tributaries. Method The study is based on water quality data collected from 2008 to 2018 from 16 monitoring sections within the basin. Various methods, including the comprehensive water quality index (WQI), water pollution index (WPI), and comprehensive water quality identification index (Iwq), were used to assess water quality. Additionally, statistical methods including the Mann- Kendall trend test, cluster analysis, and discriminant analysis were utilized to analyze the spatiotemporal variation in water quality. Result In flooding and non-flooding seasons, the section proximal to the Leshan Minjiang Bridge had minimum dissolved oxygen (DO) concentration, which is 2.86 mg/L and 3.16 mg/L, respectively. Conversely, the Nanchang Chucha section had maximum concentration of chemical oxygen demand (CODMn) and ammonia nitrogen (NH3-N), which was 10.00 mg/L and 6.45 mg/L, and 2.23 mg/L and 4.48 mg/L, respectively. In the nonflooding season, 31.82% of water in the Nanchang Chucha section achieved Class IV grade or higher (evaluated by WPI), whereas this figure reduced to 19.70% (evaluated by WQI) for the Leshan Minjiang Bridge section. The Iwq method yielded the highest water quality, followed by WQI and WPI. All three methods indicated that water quality had improved in the Leshan Minjiang Bridge, Changsha Xingang, and Nanchang Chucha sections. Water quality varied spatially, with poor quality observed in the Leshan Minjiang Bridge, Changsha Xinkang, and Nanchang Chucha sections, and slightly poor quality was found in the Minjiang, Xiangjiang, and Ganjiang sections. Conclusion The evaluation of water quality using different methods within the Yangtze River basin yielded varied results, with the WQI method working best. [ABSTRACT FROM AUTHOR]