Atomic-and nanometer-scale features of nanomaterials have a strong influence on their chemical and physical properties and a detailed description of these elements is a crucial step in their characterization. Total scattering methods, in real and reciprocal spaces, have been established as fundamental techniques to retrieve this information. Although the impact of microstructural features, such as defectiveness of different kinds, has been extensively studied in reciprocal space, disentangling these effects from size-and morphology-induced properties, upon downsizing, is not a trivial task. Additionally, once the experimental pattern is Fourier transformed to calculate the pair distribution function, the direct fingerprint of structural and microstructural features is severely lost and no modification of the histogram of interatomic distances derived therefrom is clearly discussed nor considered in the currently available protocols. Hereby, starting from atomistic models of a prototypical system (cadmium selenide), we simulate multiple effects on the atomic pair distribution function, obtained from reciprocal space patterns computed through the Debye scattering equation. Size and size dispersion effects, as well as different structures, morphologies, and their interplay with several kinds of planar defects, are explored, aiming at identifying the main (measurable and informative) fingerprints of these features on the total scattering pattern in real and reciprocal spaces, highlighting how, and how much, they become evident when comparing different cases. The results shown herein have general validity and, as such, can be further extended to other classes of nanomaterials.