Zygophyllum fabago grows in arid, saline soil, or disturbed sites, such as former industrial or mining areas. This species is able to grow in coarse mineral substrates contaminated with heavy metals. To investigate the effects of the flavonoid rutin (Rtn) on certain heavy metal stress responses such as antioxidant defense systems and water status, seedlings were subjected to 100 and 200 μM CdCl2 treatment without or with 0.25 and 1 mM Rtn for 7 and 14 d (days). Cd stress decreased growth (RGR), water content (RWC), leaf osmotic potential (ΨΠ), and chlorophyll fluorescence, all of which could be partly alleviated by addition of Rtn. Activities of superoxide dismutase, peroxidase (POX), ascorbate peroxidase, and glutathione reductase increased within the first 7 d after exposure to Cd. However, failure of antioxidant defense in the scavenging of reactive oxygen species (ROS) was evidenced by an abnormal rise in superoxide anion radical ( O2•-) and hydrogen peroxide contents and a decline in hydroxyl radical (OH•) scavenging activity, resulting in enhancement of lipid peroxidation (TBARS) as a marker of Cd-induced oxidative stress. However, exogenously applied Rtn considerably improved the stress tolerance of plants via a reduction in Cd accumulation, modulation of POX activity, increase of proline (Pro) content, decrease in TBARS and ROS content and consequent lowering of oxidative damage of membrane. Overall, 0.25 and 1 mM Rtn could protect Z. fabago from the harmful effects of 100 μM Cd-induced oxidative stress throughout the experiment.