► Water sources of tree growing on continuous and isolated outcrops were different. ► Water sources of shrub growing on continuous and isolated outcrops were the same. ► Trees on continuous outcrops and nearly thin soils had different water use patterns. ► Shrubs on outcrops and nearby thin soils both relied on shallow water sources. In the seasonally dry karst region of Southwest China, woodland vegetation is frequently associated with rocky outcrops. We used stable isotope techniques to determine the water sources of two woody plant species (the semideciduous tree Rademachera sinica and the deciduous shrub Alchornea trewioides) across three surface types: continuous and isolated dolomite outcrops, as well as adjacent surfaces with soils. Main water sources for R. sinica growing on the continuous outcrops shifted from deep water sources (e.g., water in the saturated zone) on March 23, 2009 (the late dry season of 2008–2009) to rainwater stored in rock fissures of the unsaturated zone on November 8, 2009 (the early dry season of 2009–2010). R. sinica growing on nearby thin soils exhibited a similar shift of main water sources, from deep water sources in the late dry season to shallow soil water (0–30 cm) in the early dry season. However, they extracted deep water sources from the bottom of nearby outcrops rather than from deeper layers below the soil surface. Main water sources for R. sinica growing on the isolated outcrops shifted from previous (one to two months ago) rainwater in the late dry season to the mixture of recent (within the last one month) and previous rainwater in the early dry season, while using little or no deep water sources. In contrast, A. trewioides growing on these two kinds of outcrops always relied on recent rainwater, while those growing on soils always relied on shallow soil water. The shift of water sources for tree species (especially those growing on continuous rock outcrops and nearby soils) may allow them to maintain normal transpiration throughout the year, which increases the amount of evapotranspiration in the watershed and further enhances the water storage capacity of the study area.