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The relationships between water yields of tributaries and coverage of different vegetation types in the corresponding sub-watersheds were investigated during the wet season in the Heishui River Valley, located in the upper portion of the Yangtze River in western China. Stable isotope analysis was used to calculate the relative contributions of the tributaries to water yield in the main stem of the Heishui River, while relative coverages of the different vegetation types were calculated from classified Landsat 7 TM satellite images of the study area. We found that all the sub-watersheds were dominated by two vegetation types (subalpine forest and alpine shrub-meadow) which influenced water yields in opposite ways. Lower subalpine forest coverage was significantly associated with higher tributary water yield, whereas lower alpine shrub-meadow coverage was associated with lower tributary water yield. Comparing our results to similar studies at different spatial scales, we found increasing uncertainty in the relationship between vegetation coverage (total and individual community types) and water yields as scale increased. Nevertheless, the quantitative relationships found in our study may prove useful at the appropriate scales by allowing policy makers and managers to use vegetation coverage as an indicator or index of water yield when attempting to manipulate the vegetation of watersheds to reduce the risk of flooding in this region.