The impact of landscape on river water quality varies in different regions and different spatial scales. This study was conducted along Chishui River Watershed. We divided the study area into Karst landform and Non-Karst. The basin was divided into 29 sub-watersheds, Water samples were collected for monitoring of water quality. Water variables include DO, EC, TN and TP. The choice of landscape indices was at three scales based on previous research. We used Fragstas 4.5 software to obtain landscape indices of each watershed, then performed a correlation analysis. The Spatial analysis and mathematical statistic methods were used to reveal the differences between landscapes under geomorphic regions in the basin, and explore the linkage between landscape and water quality in different spatial scales. The results show that:(1) The landscape composition in the basin is dominated by forest and shrub, followed by construction land and cultivated land. The Landscape composition has a difference in different spatial scales under different geomorphic regions. Construction land and cultivated land have negative impact on water quality, and the impact on water quality is more significant in carbonate rock areas. Forest has a positive impact on water quality. The impact of shrub on water quality is relatively complex. (2) Water quality in clastic rock area is better then that in carbonate rock area. The landscape fragmentation and TN, TP showed a positive correlations;The Landscape aggregation is positively correlated with DO;The relationship between landscape fragmentation and landscape aggregation and EC are opposite in both regions. (3) The Landscape in different geomorphic regions have different effects on river water quality. Landscape composition of riparian scale can well explain 53.4% and 59.1% of the variation of water quality respectively. Landscape pattern of riparian scale can explain 62.9% in carbonate rock area, and explain 82.4% in circular buffer in clastic rock area. Therefore, different landscape optimization measures should be taken in different geomorphic regions to reduce water pollution in Chishui River basin.