Alluvial floodplain forests have been reduced drastically in many parts of Europe, due to deforestation, the transformation to settlement and expansion of agricultural areas. Although they have been heavily modified for centuries, generalized frameworks for their management are scarce and the complex interactions between the physical environment and biological processes are often not fully understood. As the zonation of woody species in floodplains is mainly determined by hydrological conditions, flooding tolerance can be regarded as a key factor for the successful establishment of woody species. Furthermore, the oxygen level of the flooding water might affect the responses to flooding. We examined the influence of flooding duration in combination with oxygen supply by aeration on the foliar injury and growth of six-week-old saplings of ten woody species, under controlled common garden conditions. Six of them are considered to be flooding tolerant whereas four are intolerant. In addition, seven are native whereas three are non-native species. During the experiment, the saplings were exposed to partial flooding of different durations (k = 3; three, six and nine weeks) and oxygen levels (k = 2; aerated and not aerated). For comparison, we included an unflooded control. We recorded foliar injury, plant height, number of leaves and stem diameter. We also included a long-term recovery period. Whereas foliar injury decreased for most species with increasing flooding duration, the typical floodplain forest species, classified as flooding tolerant developed better. The differences in species response to flooding could be most likely explained by their ability to react to the resulting stress in morphological, physiological and metabolic terms irrespective whether they are native or not. In addition, the inclusion of a recovery period seems to be important for the assessment of flooding tolerance.