Charge-coupled device (CCD)-based technologies exposed to high-energy radiation are susceptible to the formation of stable defects within the charge transfer channel that defer signal to subsequent pixels and limit the lifetime of the detector. Performance degradation due to these defects depends upon the interplay between the clock timings used to operate the device and the properties of defects introduced by irradiation. Characterization of both the type and number of post-irradiation defects makes it possible to minimize charge loss though the appropriate selection of clock timings for a given operating temperature. This technique has the potential to increase nominal mission lifetimes by several years for CCD-based instruments and is of particular significance to electron multiplying charge-coupled devices (EMCCDs) for photon counting applications where the effect of charge traps on low signal levels is expected to be most severe. We present a study of charge traps within CCDs, specifically within EMCCDs irradiated at room temperature to proton fluences up to and including 1.45  ×  10¹⁰  p⁺  /  cm² (74 MeV). Defects are characterized through the “single-trap pumping” technique, with clocking schemes specifically designed for the 2-phase pixel architecture of the EMCCD. Five dominant trap species are thought to be introduced by the irradiation, the Si-E center, Si-A center, double and single acceptor charge states of the silicon divacancy (VV^{−    −}, VV⁻), and an as yet unidentified defect referred to here as the Si-U center (the “unknown” trap). Energy-level and cross-section values are presented that allow inference of the defect landscape for a range of proton fluences and operating temperatures. While the study focuses specifically on EMCCDs, in more general terms, the results for trap properties are interpreted as being applicable to all CCD types following irradiation and can serve as a foundation for future charge loss correction and optimization techniques.