Abstract The signatures of photon and charged particle interactions in an X-ray CCD have been investigated and techniques for reducing spectral data developed. It is found that the energy-loss spectrum of X-rays which interact in the depletion layer are well described by simple functions and show little evidence of redistributive processes. However, photons which interact in the “so-called” field-free region introduce multi-pixel, line-like features into the spectral data which are shifted in energy and slightly broadened with respect to depletion region events. The efficiency of this process can be surprisingly high, being comparable to the depletion layer efficiency at 10 keV for the devices considered in this study. For astrophysical applications, these artifacts can have energies and intensities comparable to expected non-solar line and edge features. We have developed procedures to identify, quantify and correct for these effects to arbitrary precision. Simple statistical techniques are described to ascertain when, and if, they need to be applied.