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Hydrophilic silicon carbide was modified by surface deposition of a super-hydrophobic coating that is based on perfluorosilanes. The modification was proven to yield membrane surfaces with contact angles that were higher than 145° and to be stable under hydrothermal conditions. The measurement of the isosteric heat of adsorption of water and toluene by microgravimetry showed that, after modification, the membrane material was fully covered by a low-energy surface, which is consistent with the fluorocarbon moieties that were introduced by the modification. The same modification method was applied to a commercial multichannel SiC membrane tube (nominal pore size = 0.04 µm), which was tested in a direct contact membrane distillation apparatus. The membrane was permeable to water vapour and volatiles, but it showed full rejection for salt ions and organic pollutants with low vapour pressure (such as ibuprofen and caffeine). Moreover, the membrane was reusable, and its performances were stable with no sign of pore wetting over 8 h of filtration.