Understanding the responses of riparian trees to water availability is critical for predicting the effects of changes in precipitation on riparian ecosystems. Dioecious Acer negundo L. (box elder) is a common riparian tree that is highly sensitive to water stress. Earlier studies indicated that the genders of A. negundo respond differently to water availability, with males being more conservative in their water use than females. To assess the potential effects of changes in precipitation on the sex ratio of riparian trees, we extended earlier studies of A. negundo by analyzing responses of male and female genotypes to interannual differences in water availability in a common garden. We measured growth of tree rings and used stable carbon isotope analysis of tree ring alpha-cellulose to integrate physiological responses to annual water treatments. During dry years, male and female trees exhibited similar growth and physiological responses. However, during wet years, females exhibited higher growth rates and lower carbon isotope ratios (indicating less conservative water use) than did males. Furthermore, we found that male trees exhibited similar stomatal behavior (inferred from integrated carbon isotope ratios) whether years were wet or dry, whereas females did not exhibit a consistent response to changes in water availability. We predict that with increasing precipitation and soil water availability, the representation of females will be favored because of shifts in the competitive interactions of the genders. Such changes may affect the reproductive output of these riparian trees and may influence overall water flux from riparian ecosystems. In addition, this study demonstrates the utility of carbon isotope analysis for assessing long-term responses of tree populations to shifts in water availability.