Imidazolium-based ionic liquids (ILs) are frequently used solvents, due to their peculiar structure resulting in low melting points. Recent studies revealed the direct impact of the water molecules on the self-structuring of the IL nano-domains. Therefore, in this work the influence of different water impurities on the IL network and its vacuum stability has been studied using Nuclear Magnetic Resonance (NMR) and Electrochemical Impedance Spectroscopy (EIS). As a result, three distinguishable interdependent regions could be identified. Degassing of solutions with different IL-H2O ratios proved a strong dependence of the removed water species on the initial composition of the doped IL nano-domains. Consequently, selective purification of targeted cavities, based on vacuum extraction, is proposed as a novel tool to control the structural rearrangement of the ionic liquid networks in the presence of water.