The influence of aquaporin (AQP) activity on plant water movement remains unclear, especially in plants subject to unfavorable conditions. We applied a multitiered approach at a range of plant scales to (i) characterize the resistances controlling water transport under drought, flooding, and flooding plus salinity conditions; (ii) quantify the respective effects of AQP activity and xylem structure on root (K-root), stem (K-stem), and leaf (K-leaf) conductances; and (iii) evaluate the impact of AQP-regulated transport capacity on gas exchange. We found that drought, flooding, and flooding plus salinity reduced K(root )and root AQP activity in Pinus taeda, whereas K-root of the flood-tolerant Taxodium distichum did not decline under flooding. The extent of the AQP control of transport efficiency varied among organs and species, ranging from 35-55% in K-root to 10-30% in K-stem and K-leaf. In response to treatments, AQP-mediated inhibition of K root rather than changes in xylem acclimation controlled the fluctuations in K-root. The reduction in stomata! conductance and its sensitivity to vapor pressure deficit were direct responses to decreased whole-plant conductance triggered by lower K-root and larger resistance belowground. Our results provide new mechanistic and functional insights on plant hydraulics that are essential to quantifying the influences of future stress on ecosystem function.