Recruitment of plant species in wetlands dominated by Phragmites australis often results in a zonation of two vegetation types. A development of reed marshes takes place in the shallow flooded parts where the dominant P. australis becomes accompanied by interstitial marsh species. The vegetation on higher elevations becomes dominated by tall forbs. We investigated whether this zonation is related to the effects of flooding on the recruitment of component species of both vegetation types. All but one species had maximum germination at field capacity and germination was strongly reduced in drier soils and flooded soils. Nearly all seedlings of reed marsh species, irrespective of whether they initially supported two or six true leaves, survived eight weeks of total inundation. Survival of tall forbs was however significantly decreased by inundation. At both seedling stages a considerable number of Cirsium arvense lost their leaves when submerged, but all plants were able to recover when drained. Eupatorium cannabinum suffered extra mortality when transferred from flooded to drained conditions, whereas only young seedlings of Epilobium hirsutum died. Of all investigated species E. hirsutum was the only one with a significantly increased stem length after one week of submergence. Root porosities did not differ between reed marsh species and tall forbs but stem porosities of the reed marsh species Mentha aquatica and Lycopus europaeus were significantly higher than those of the tall forbs C. arvense and E. cannabinum. It was concluded that both reed marsh species and tall forbs require lowered water levels for germination. Flooding during the seedling stage will assign species to their position on the elevation gradient. Reed marsh species establish at lower elevations because they are best able to survive flooding and because their higher stem porosities allows them to withstand higher levels of partial submergence.