We used grazing-incidence small-angle neutron scattering (GISANS) to probe the depth-dependent orientation of self-assembled morphologies of block copolymers. A hydrophobic–hydrophobic block copolymer, poly(solketal methacrylate)-block-polystyrene (PSM-b-PS), was synthesized and spin-coated into films tens of nanometers in thickness where the polymers adopted a disordered state. PSM-b-PS was then hydrolyzed by exposing the polymer thin film to trifluoroacetic acid vapor or embedding a photoacid generator in the film during spin coating, followed by exposure to UV light. The hydrolysis converted the block copolymer into a hydrophilic–hydrophobic block copolymer, poly(glycerol monomethacrylate)-block-polystyrene (PGM-b-PS), significantly increasing the segmental interaction parameter (χ) and causing microphase separation of the copolymers. GISANS was used to study the depth-dependent structure of the films and revealed that the orientation of the microphase-separated structure differed at the polymer–air and polymer–substrate interfaces. In the regions where the lamellae were parallel to the interfaces, the orientation propagated into the film from the interfaces. However, in the areas where the lamellae were perpendicular to the interfaces, the orientation did not persist with increasing distance from the interfaces.