We discuss a potentially dramatic source of quantum decoherence in three-dimensional niobium superconducting resonators and in two-dimensional transmon qubits that utilize oxidized niobium: an aggravation of two-level system (TLS) induced losses driven by vacuum baking at temperatures and durations typically used in transmon qubit fabrication. By coupling RF measurements on cavities with time-of-flight secondary ion mass spectrometry studies on an SRF cavity cutout, we find that modest vacuum baking (150-200~$^{circ}$C for 5~min-11~hrs) produces a partially depleted native niobium oxide which likely contains a large concentration of oxygen vacancies that drive TLS losses. Continued baking is found to eliminate this depleted layer and mediate these additional losses.
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