An improved understanding of the mechanisms underlying plant adaptation to habitat heterogeneity can be achieved by clarifying the climate-driving factors of the hydraulic and photosynthetic traits of different populations. With a focus on Populus pruinosa Schrenk, which is the predominant tree species in the desert riparian forests of the Tarim Basin, Xinjiang, this study investigated the hydraulic and photosynthetic trait relationships and their interactions with environmental factors in 11 P. pruinosa populations using a Pearson correlation analysis, plant trait networks, a redundancy analysis, and a least squares linear regression analysis. The results showed that the degree of variation in the hydraulic traits was higher than that in the photosynthetic traits. The net photosynthetic rate (Pn) showed a significantly positive correlation with leaf-specific conductivity (Kl) and the Huber value (Hv). The Hv exhibited a significantly positive correlation with the water-use efficiency and Kl, and the branch–leaf mass ratio significantly affected the hydraulic traits. The groundwater depth (GD) in natural P. pruinosa forest habitats ranged from 3.4 to 7.9 m. With an increase in the annual average temperature, the hydraulic conductivity of the xylem significantly increased; with an increase in GD, Pn and Kl significantly decreased. The temperature annual range, temperature seasonality (standard deviation), min temperature of the coldest month, and GD were significantly correlated with the diameter and average path length of the overall trait network parameters, and these environmental factors affected the coordination of the functional traits of P. pruinosa.