Although cell membranes in physiological conditions exist in excess of water, there is a number of biochemical processes, such as adsorption of biomacromolecules or membrane fusion events, that require partial or even complete, transient dehydration of lipid membranes. Even though the dehydration process is crucial for understanding all fusion events, still little is known about the structural adaptation of the lipid membranes when their interfacial hydration layer is perturbed. Here, we introduce the study on the nanoscale structural reorganization of the phase-separated, supported lipid bilayers (SLBs) under a wide range of hydration conditions. Model lipid membranes were characterized with the combination of fluorescence microscopy and atomic force microscopy, and crucially, without applying any chemical or physical modifications, that so far have been considered to be indispensable for maintaining the membrane integrity upon dehydration. We revealed that decreasing hydration state of the membrane leads to an enhanced mixing of lipids characteristic for the liquid-disordered (Ld) phase with those forming liquid-ordered (Lo) phase. This is associated with a 2-fold decrease in the hydrophobic mismatch between the Ld and Lo lipid phases and a 3-fold decrease of line tension for the completely desiccated membrane. Importantly, the observed changes in the hydrophobic mismatch, line tension, and miscibility of lipids are fully reversible upon subsequent rehydration of the membrane. These findings provide deeper insights into the fundamental processes such as cell-cell fusion that require partial dehydration at the interface of two membranes.