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The characterization of quantum processes, e.g. communication channels, is an essential ingredient for establishing quantum information systems. For quantum key distribution protocols, the amount of overall noise in the channel determines the rate at which secret bits are distributed between authorized partners. In particular, tomographic protocols allow for the full reconstruction, and thus characterization, of the channel. Here, we perform quantum process tomography of high-dimensional quantum communication channels with dimensions ranging from 2 to 5. We can thus explicitly demonstrate the effect of an eavesdropper performing an optimal cloning attack or an intercept-resend attack during a quantum cryptographic protocol. Moreover, our study shows that quantum process tomography enables a more detailed understanding of the channel conditions compared to a coarse-grained measure, such as quantum bit error rates. This full characterization technique allows us to optimize the performance of quantum key distribution under asymmetric experimental conditions, which is particularly useful when considering high-dimensional encoding schemes.