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In this study, we have considered the relationship between the spatial configuration of land use and water quality in the Three Gorges Reservoir Area. Using land use types, landscape metrics, and long-term water quality data, as well as statistical and spatial analysis, we determined that most water quality parameters were negatively correlated with non-wood forest and urban areas but were strongly positively correlated with the proportion of forest area. Landscape indices such as patch density, contagion, and the Shannon diversity index were able to predict some water quality indicators, but the mean shape index was not significantly related to the proportions of farmland and water in the study area. Regression relationships were stronger in spring and fall than in summer, and relationships with nitrogen were stronger than those of the other water quality parameters (R ² > 0.80) in all three seasons. Redundancy analysis showed that declining stream water quality was closely associated with configurations of urban, agricultural, and forest areas and with landscape fragmentation (PD) caused by urbanization and agricultural activities. Thus, a rational land use plan of adjusting the land use type, controlling landscape fragmentation, and increasing the proportion of forest area would help to achieve a healthier river ecosystem in the Three Gorges Reservoir Area (TGRA).