Tree transpiration dynamics and mechanisms in karst habitats are not fully understood due to the heterogeneous environmental features and complex species composition. Two common coexisting tree species, Mallotus philippensis and Celtis biondii, were examined in soil- and rock-dominated (SD and RD) karst habitats. Soil moisture, plant transpiration, root distribution, and leaf water potential were measured over two years (2021 and 2022). The mean water content was significantly lower in the RD than in the SD habitat. Transpiration patterns also differed between habitats, although species-specific distinctions were driven by leaf and root physiological traits. M. philippensis showed an isohydric tendency in both habitats and a lower density of fine roots, mostly in the soil zone, in the RD habitat. The transpiration of M. philippensis followed the variation in soil moisture, being lower in the RD habitat. Conversely, an anisohydric tendency in both habitats and a higher density of fine roots in both the soil and bedrock zones in the RD habitat were found in C. biondii. This species showed higher transpiration in the RD habitat, arising from ample water availability from soil and epikarst. Our findings reveal the regulatory mechanisms of species-specific root-zone water availability in transpiration patterns across karst habitats.