There is considerable interest in naturalizing flow regime on managed rivers to slow the spread of saltcedar (Tamarix ramosissima) invasion in southwestern USA or to preserve riparian forests dominated by saltcedar and other species in northwestern China. However, little is known about the responses of established saltcedar in water sources to frequent intra‐annual fluctuation of water table resulting from this new, more dynamic flow regime. This study investigates how saltcedar at a riparian site in the middle reaches of the Heihe River, northwest China, responds in water sources use to intra‐annual water table fluctuations. Stable oxygen isotope was employed to determine accurate depth at which saltcedar obtains its water supply, and soil moisture monitoring was used to determine sources of plant‐available soil water. We found that the primary zone of water uptake by saltcedar were stable at 25–60 cm depth, but the water sources used by saltcedar switched between groundwater and soil moisture with the water table fluctuations. Saltcedar derived its water from groundwater when water table was at depth less than 60 cm but switched to soil moisture at 25–60 cm depth when water table declined. It is supposed that the well‐developed clay layer at 60–80 cm depth constrained lateral roots of saltcedar to the soil layers above 60 cm, while the fine‐textured soils at this site, which were periodically resaturated by rising groundwater before the stored soil moisture had become depleted, provided an important water reservoir for saltcedar when groundwater dropped below the primary zone of fine roots. The root distribution of saltcedar may also be related to local groundwater history. The quick decline in water table in the early 1980s when the riparian saltcedar had established may strand its roots in the shallow unsaturated zone. We suggested that raising the water table periodically instead of maintaining it invariably above the rooting depth could sustain desired facultative phreatophytes while maximizing water deliveries. Copyright © 2015 John Wiley & Sons, Ltd.