In the Mediterranean basin, Tamarix spp. constitute important populations along rivers and sea coasts, and might be primarily subjected to water level fluctuations and salinization, as a consequence of global climate change. Here, we analyze leaf gas exchange and xylem anatomy during a water level decrease below the soil surface after short‐term flooding with fresh‐ and saline‐water (200 mM) in order to predict Tamarixafricana Poiret responses under future environmental conditions. Fresh‐water level reduction negatively affected stomatal conductance (−56.3 %), but only when water decreased to the lowest level (15 cm below the soil surface). No effects on assimilation rates and xylem vessel dimensions occurred. Under saline conditions, the rate of the water level decrease was lower compared to the non‐saline treatment, as stomatal conductance was negatively affected by salinity (−59.5 %) and significantly declined over time. Moreover, decreases in mean xylem vessel area (−51.3 %), assimilation rates (−52.2 %) and stomatal conductance (−76.0 %) were also observed compared to the control, indicating both an osmotic stress and a toxic effect of NaCl on leaf gas exchange. These leaf responses were probably induced by greater belowground‐root salt absorption and transport compared to previous flooding conditions, as confirmed by the increase in salt excretion (+473.2 %). The results emphasize the survival risk of Tamarix spp. to water level variation under both saline and non‐saline conditions, and the need of management practices focused on the conservation of these populations.