Sustainable water management requires an understanding of the effects of flow regulation on riparian eco-morphological processes. We investigated the transient response of Salix viminalis by examining the effect of water level regimes on its above and below-ground biomass. Four sets of Salix cuttings, three juveniles (in the first growing season) and one mature (one year old), were planted and initially grown under the same water-level regime for one month. We imposed three different water level regime treatments representing natural variability, a seasonal trend with no peaks, and minimal flow (characteristic of hydropower) consisting of a constant water level and natural flood peaks. We measured sap flux, stem water potential, photosynthesis, growth parameters, and final root architecture. The mature cuttings were not affected by water table dynamics, but the juveniles displayed causal relationships between the changing water regime, plant growth, and root distribution during a two-month transient period. For example, a 50% drop in mean sap flux corresponded with a −1.5 Mpa decrease in leaf water potential during the first day after the water regime was changed. In agreement with published field observations, the cuttings concentrated their roots close to the mean water table of the corresponding treatment, allowing survival under altered conditions and resilience to successive stress events. Juvenile development was strongly impacted by the minimum flow regime, leading to more than 60% reduction of both above- and below-ground biomass, with respect to the other treatments. Hence, we suggest avoiding minimum flow regimes where Salix restoration is prioritized. This article is protected by copyright. All rights reserved.