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The wettabilities of nanoscale porous surfaces play important roles in the context of molecular and fluid transport or oil–water separation. The wettability pattern along a nanopore strongly influences fluid distribution throughout the membrane. Mesoporous silica thin films with gradually adjusted wettabilities were fabricated via cocondensation. With consecutive mesoporous layer depositions, double-layer mesoporous silica films with asymmetric or so-called Janus wettability patterns were generated. The effects of these wetting gradients on mass transport, water imbibition, and water vapor condensation were investigated with ellipsometry, cyclic voltammetry (CV), drop friction force instrument (DoFFIs), fluorescence microscopy and interferometry. By increasing the film thickness of the hydrophobic mesoporous silica top layer deposited on a hydrophilic mesoporous silica layer up to 205 nm, molecular transport through both the layers was prevented. However, water was observed to condense onto the bottom layer, and transport occurred for thinner top layers.