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The analysis of x-ray reflectivity data from artificial heterostructures usually relies on the homogeneity of optical properties of the constituent materials. However, when the x-ray energy is tuned to the absorption edge of a particular resonant site, this assumption may no longer be appropriate. For samples realizing lattice planes with and without resonant sites, the corresponding regions containing the sites at resonance will have optical properties very different from regions without those sites. In this situation, models assuming homogeneous optical properties throughout the material can fail to describe the reflectivity adequately. As we show here, resonant soft x-ray reflectivity is sensitive to these variations, even though the wavelength is typically large as compared to the atomic distances over which the optical properties vary. We have therefore developed a scheme for analyzing resonant soft x-ray reflectivity data, which takes the atomic structure of a material into account by ‘slicing’ it into atomic planes with characteristic optical properties. Using LaSrMnO₄ as an example, we discuss both the theoretical and experimental implications of this approach. Our analysis not only allows to determine important structural information such as interface terminations and stacking of atomic layers, but also enables to extract depth-resolved spectroscopic information with atomic resolution, thus enhancing the capability of the technique to study emergent phenomena at surfaces and interfaces.