The performance of seedlings is crucial for the survival and persistence of plant populations. Although drought frequently occurs in floodplains and can cause seedling mortality, studies on the effects of drought on seedlings of floodplain grasslands are scarce. We tested the hypotheses that drought reduces aboveground biomass, total biomass, plant height, number of leaves, leaf area and specific leaf area (SLA), and increases root biomass and root-mass fraction (RMF) and that seedlings from species of wet floodplain grasslands are more affected by drought than species of dry grasslands. In a greenhouse study, we exposed seedlings of three confamilial pairs of species (Pimpinella saxifraga, Selinum carvifolia, Veronica teucrium, Veronica maritima, Sanguisorba minor, Sanguisorba officinalis) to increasing drought treatments. Within each plant family, one species is characteristic of wet and one of dry floodplain grasslands, confamilial in order to avoid phylogenetic bias of the results. In accordance with our hypotheses, drought conditions reduced aboveground biomass, total biomass, plant height, number of leaves and leaf area. Contrary to our hypotheses, drought conditions increased SLA and decreased root biomass and RMF of seedlings. Beyond the effects of the families, the results were species-specific (V. maritima being the most sensitive species) and habitat-specific. Species indicative of wet floodplain grasslands appear to be more sensitive to drought than species indicative of dry grasslands. Because of species- and habitat-specific responses to reduced water availability, future drought periods due to climate change may severely affect some species from dry and wet habitats, while others may be unaffected.