Growing on sands, Alyssum desertorum does not need to adapt to long-term waterlogging. To assess the ability of this psammophyte to tolerate excessive moisture, we studied the responses of plants to root flooding. Seeds were collected from plants of the dry sandy areas of ravine forests in the Steppe Zone of the Dnipropetrovsk region, Ukraine. Three-week-old plants grown on sandy soil were subjected to soil flooding for 10 days. Heat shock protein HSP70 as a marker of stress reaction, alcohol dehydrogenase (ADH) as a key enzyme of anaerobic adaptation, photosynthetic pigment level, and ethylene as a phytohormone of hypoxic response and senescence were analyzed. A weak differential induction of two HSP70 isoforms (70 kDa and 73 kDa) simultaneously with the absence of significant changes in the total protein spectrum was determined, which indicates the role of chaperones in maintaining cellular proteostasis. At the same time, the rapid temporary activation of ADH synthesis in leaves during the first two days showed short-term systemic anaerobic metabolic adaptation to root hypoxia. On the other hand, the progressive increase in ethylene emission and decrease in pigment content were, rather, associated with induced plant senescence. The obtained data showed that this psammophyte has adaptive molecular mechanisms that enable it to survive short-term soil flooding.