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The water quality of the basin is affected by many factors. The unique geological conditions in karst areas create highly heterogeneous geographical characteristics, which makes the relationship between water quality and landscape more complex and uncertain. In order to further study how these factors affect water quality in typical karst basin, this study takes Chishui River Basin in Southwest China as the research object, and Kruskal-Wallis test, Pearson correlation analysis and geographic detector methods were used to quantitatively explore the difference between STR and LTR water quality factors and the impact of landscape on water quality under the driven of temperature, precipitation, population density and per capita GDP. The novelty of this study is that according to the topographic and geomorphic features of Chishui River Basin, sub-basins with different topographic relief are divided to study the difference of the influence of surface landscape on river water quality driven by topography, meteorology and human activities. The results show that: (1) The water quality in the area with large topographic relief (LTR) is better than that in the area with small topographic relief (STR); (2) In STR, human activities are more obvious, and dry land and construction land have a significant impact on water quality; In LTR, forest land is the main factor; (3) In STR, the interaction between population density and landscape indicators is obvious, while in LTR, the interaction between precipitation and landscape indicators is significant; (4) In STR, the focus is to coordinate the relationship between natural landscape types and man-made landscape types; In LTR, it is more necessary to harness steep slope farmland. Understanding the influencing factors of water quality in different topographic relief areas can determine more targeted protection measures in different topographic relief areas to achieve the purpose of protecting water quality.