Groundwater is a critical moisture source for the growth and survival of dryland forests. Spatiotemporal variations in water table depth (WTD) affect soil water availability in the root zone, which influences canopy transpiration (Ec). However, to date, relatively few studies have been conducted on how changes in WTD regulate Ec. We measured the meteorological variables, volumetric water content (VWC), sap flow, and WTD in 2022 and 2023 from April to October in three Mongolian pine plantations located in Mu Us Sandy Land, China. The initial WTDs were 4 m (WTD4), 9 m (WTD9), and 13 m (WTD13), respectively. The mean VWC did not differ significantly between WTD4, WTD9, and WTD13 in the 0–50 cm layer. However, there was a significant decrease in the mean VWC with increasing WTD in the 50–200 cm layer (p < 0.05). Ec decreased significantly with increasing WTD (p < 0.01), with mean daily Ec of 1.25, 0.75, and 0.28 mm day−1 for WTD4, WTD9, and WTD13, respectively. Under soil drought conditions, Ec decreased significantly at WTD9 and WTD4 (p < 0.05). Meanwhile, Ec at WTD13 did not vary significantly under the different soil moisture conditions. At WTD9 and WTD13, Ec was mainly influenced by VWC. Meanwhile, at WTD4, Ec was influenced by the vapor pressure deficit and solar radiation. The diameter at breast height and leaf area index at WTD13 were significantly lower than those at WTD9 and WTD4 (p < 0.05). Although Mongolian pine could alleviate soil drought by adjusting Ec through morphological and physiological adaptations, it still suffered from the adverse effects of reduced water availability at deep WTD sites. This study establishes a basis for predicting the response of forests in semi-arid areas to changes in WTD. It contributes to the optimization of silvicultural design in similar areas and reduces ecological risks from the over-exploitation of groundwater.