Mauritia flexuosa is an ecologically and economically important Amazonian palm. It has an expanded distribution to flooded ecosystems (“veredas”) in the markedly seasonal Cerrado biome. The species' seeds are sensitive to desiccation, which limits the formation of soil seed banks, although there are indications that M. flexuosa can form seedling banks in microenvironments subject to water stress conditions. We evaluated this issue considering both morphological and physiological seedling responses to water availability. Mauritia flexuosa seedlings were grown in soils taken from the bottom (organosol) and the edge (gleisol) of a seasonally flooded vereda ecosystem with 0, 40, 60, 80 and 100% available water contents, and their survival and morphologies were evaluated for eight months. At the end of this period, dry mass, photosynthetic parameters, ABA content, leaf ultrastructure, and gene expression associated with aquaporins (MIP family) were evaluated. The seedlings showed phenotypic plasticity, with positive responses to water availability (growth and photosynthetic parameters) as well as the notable ability to survive under water stress in both of the soil types examined. Their responses to water stress were related to ABA accumulation and the maintenance of water homeostasis – with modulation of stomatal control, water use efficiency, and MIP gene expression. Mauritia flexuosa can form seedling banks in both flooded and water-stressed environments, which contributes to its reproductive success and wide distribution. The introduction of seedlings produced ex situ could be a viable alternative for the recovery of degraded areas.