Reserves of non-structural carbohydrates (NSC) stored in living cells are essential for drought tolerance of trees. However, little is known about the phenotypic plasticity of living storage compartments (SC) and their interactions with NSC reserves under changing water availability. Here, we examined adjustments of SC and NSC reserves in stems and roots of seedlings of two temperate tree species, Acer negundo L. and Betula pendula Roth., cultivated under different substrate water availability. We found that relative contents of soluble NSC, starch and total NSC increased with decreasing water availability in stems of both species, and similar tendencies were also observed in roots of A. negundo. In the roots of B. pendula, soluble NSC contents decreased along with the decreasing water availability, possibly due to phloem decoupling or NSC translocation to shoots. Despite the contrast in organ responses, NSC contents (namely starch) positively correlated with proportions of total organ SC. Individual types of SC showed markedly distinct plasticity upon decreasing water availability, suggesting that water availability changes the partitioning of organ storage capacity. We found an increasing contribution of parenchyma-rich bark to the total organ NSC storage capacity under decreasing water availability. However, xylem SC showed substantially greater plasticity than those in bark. Axial storage cells, namely living fibers in A. negundo, responded more sensitively to decreasing water availability than radial parenchyma. Our results demonstrate that drought-induced changes in carbon balance affect the organ storage capacity provided by living cells, whose proportions are sensitively coordinated along with changing NSC reserves.