Most riparian trees are phreatophytic, water table-dependent plants which broadly differ in their tolerance to drought and permanent flooding. In semi-arid settings, as water is limiting, inundations may be regarded as inputs rather than stresses for the survival of phreatophytes. In this study, the mortality rates and abundances of Populus alba, P. nigra, Salix alba and local Tamarix spp. were examined in 43 plots with different hydrologic conditions distributed across the floodplain of a large semi-arid and Mediterranean river, the Ebro River (Spain). The objectives were to determine hydrologic thresholds for the maintenance of declining populations of those species, while providing novel information on their phreatophytic nature, and to examine shifts in the species composition along hydrologic gradients. All species exhibited significant relationships between mortality rates and hydrologic variables (deepest water table—WT, flood duration—FD and flood frequency—FF). S. alba was found to be the species with lowest tolerance to drier conditions (hydrologic thresholds for maintaining a mortality rate <50%: WT > −1.22 m; FD: out of observation range; FF > 5.4 events y−1), followed by P. nigra (WT > −2.18 m; FD > 11.1%; FF > 3.8 events y−1), Tamarix spp. (WT > −2.96 m; FD > 3.7%; FF > 2.5 events y−1) and P. alba (WT > −3.45 m; FD > 1.7%; FF > 2.0 events y−1). Only a significant reduction in S. alba relative abundance was observed as conditions got drier. The results provided quantitative information useful to guide management plans for the protection of Mediterranean phreatophytic tree species from further degradation and suggested that eventual natural or regulation-induced droughts and groundwater declines would accelerate the loss of all phreatophytic species, especially S. alba. Copyright © 2010 John Wiley & Sons, Ltd.