Water adsorption in many porous optical coatings can cause a detrimental red-shift in the optical properties. In this study, a porous nanostructured rugate filter is fabricated using the glancing-angle deposition (GLAD) technique, and rendered insensitive to large changes in ambient humidity by post-deposition vapor-phase functionalization. A central defect mode is added to the stop band of the filter by integrating a phase shift into the sinusoidal refractive-index profile of the film. By monitoring the wavelength of the defect mode under variable humidity conditions, a six-times reduction in sensitivity to water vapor is observed upon functionalization with 3,3,3-trifluoropropyltrichlorosilane. Electrical characterization and advancing aqueous I contact-angle measurements are used to verify the hydrophobic properties of the functionalized thin films.