The optical properties of three-dimensional ordered superstructures formed on glass substrates by self-assembly of cadmium selenide or lead sulfide nanocrystals (NCs) are investigated and compared to the optical properties of the initial NC colloidal solutions. The formation of the superstructures is strongly correlated to the presence of oleic acid molecules on the surface of the NCs. It is found that the absorption band of the NCs in the superstructures is broadened and shifted to shorter wavelengths in comparison with the absorption band of the NCs in solution. The luminescence spectra of the NCs in the superstructures also differ from the spectra of the NCs in solution. The observed modification of optical properties of superstructures is a manifestation of interactions between the NCs and the chemical environment within the superstructures.