The neotropical palm Mauritia flexuosa produces seeds that show the association between recalcitrance and dormancy. Despite the intolerance to desiccation, the seeds can maintain persistent banks in flooded environment soils (veredas) in the Cerrado biome. As the mechanisms involved in the persistence of recalcitrant seed banks are still poorly understood, the objective of this work was to evaluate the response of M. flexuosa embryos to water deficit and saturation stresses. Embryos of M. flexuosa with water content typical of dispersion or subjected to hydration were exposed to moderate and severe water potentials (Ψw= −1.5 MPa and Ψw= −2.1 MPa), in addition to water saturation (Ψw= 0 MPa). Anatomical, histochemical and ultrastructural evaluations were performed on the embryos after 24 h. Membrane integrity estimation, endo-β-mannanase activity and oxidative stress indicators (H2O2 and MDA contents, CAT, SOD and APX activity) were also evaluated. The endosperm structure contributes to the maintenance of embryo hydration, while abundant mucilage reserves favor resilience to desiccation. Post-dispersal hydration makes embryos less vulnerable to oxidative stress, which is due to the non-enzymatic antioxidant system. Both moderate water stress and post-dispersal water absorption induce an increase in metabolism and the mobilization of reserves, which indicate that hydration/dehydration cycles can favor overcoming dormancy. M. flexuosa embryos show resilience to water deficit, and that is crucial for the persistence of seeds in the soil in seasonal environments, however, successful germination is dependent on high hydration, which prevents structural and physiological damage.