An unconventional nanoporous organosilica membrane has been tested in a vacuum membrane distillation (MD) process for water desalination. We propose a modified approach to understand the transport mechanism of water molecules through the nanopores of this membrane. The modified approach stems from the fact that the membrane has a hydrophilic surface (contact angle <90°) and so capillary pressure, which draws liquid water into the nanopore, must be considered when establishing the mathematical model. However, increased friction arising from the dramatic increase in shear viscosity of water in nano-confined spaces balances the capillary flow against the evaporative mass transport to avoid pore wetting. Notably, the liquid/vapor interface is no longer formed at the pore entrance as with a conventional hydrophobic membrane, but rather exists deeper in the pore channel as a consequence of capillary pressure. This was backed by experimental observations (no pore wetting) and SEM evidence which showed salt nucleation and growth existed only on the membrane surface, and did not infiltrate the membrane support layers. The impacts of pore size, membrane thickness, substrate thickness, concentration polarization, porosity, and contact angle on water flux and pore intrusion depth were tested using the model. Pore size was the most influential parameter with an >80% increase in permeation flux if the pore size increased from 2 to 3nm at 60°C. However, pore wetting is expected if dp>3.4nm, particularly at low temperatures where the slower evaporation rate promoted greater pore intrusion. Concentration polarization was shown to be negligible which agreed well with experimentally observed water fluxes which remained relatively constant despite feed salinity increasing from 0 to 150gL−1. Lastly, the membrane hydrophilicity was found to impact on water flux and pore intrusion in a complex relationship with pore size. Ultimately, hydrophilic pores less than 3nm in diameter offer a good combination of good water flux and minimal water intrusion suggesting that ordered mesoporous organosilica membranes have potential in MD applications.