In the present work, ultra-thin zeolite CHA and FAU membranes, with thicknesses of 600 and 500 nm, respectively, were evaluated for desalination by pervaporation at various temperatures. Single gas permeation experiments were employed to verify high quality of the membranes. At 90 °C, the observed water fluxes for CHA and FAU membranes were as high as 24 and 28 kg/(m2‧h), respectively. A mathematical model was used to estimate the effect of the support. The results showed that the mass transfer resistance of the support reduced the flux. The water flux corrected for the mass transfer resistance over the support was as high as 40 and 51 kg/(m2‧h) at 90 °C for CHA and FAU membranes, respectively. To the best of our knowledge, these are the highest reported water fluxes for desalination by zeolite membranes in a pervaporation process.