Sessile oak is a species of great ecological and silvicultural importance in Europe; however, increased frequency and severity of flooding of forested areas pose a threat to its regeneration. We monitored water relations, root anatomical changes and the expression of two calmodulin genes (QpCaM) in sessile oak seedlings during a 14-day flooding treatment. The response followed two characteristic sequences. The first phase, in response to between 1 h and 3 days of flooding, was characterized by a dramatic but transient decline in water relations parameters followed by a recovery towards control values with no noticeable change in root cell morphology. During the second phase, in response to 3 to 14 days of flooding, water relations parameters gradually and continuously declined and hypertrophied lenticels developed at the base of the shoot. Concurrently, root cortical cells became larger and less spherical and the root cortex more porous. These cellular changes were accompanied by a transient rise in root transcript levels of QpCaM-2. We conclude that sessile oak seedlings are capable of withstanding a 3-day period of flooding without significant morphological alterations. In contrast, exposure to flooding for more than 3 days resulted in anatomical and morphological changes in the root system. These changes are, however, insufficient to provide sessile oak with long-term tolerance to flooding.