Not yet reviewed by Pith; the record is open.

Qubits made from superconducting materials are a mature platform for quantum information science application such as quantum computing. However, materials-based losses are now a limiting factor in reaching the coherence times needed for applications. In particular, knowledge of the atomistic structure and properties of the circuit materials is needed to identify, understand, and mitigate materials-based decoherence channels. In this work we characterize the atomic structure of the native oxide film formed on Nb resonators by comparing fluctuation electron microscopy experiments to density functional theory calculations, finding that an amorphous layer consistent with an Nb$_2$O$_5$ stoichiometry. Comparing X-ray absorption measurements at the Oxygen K edge with first-principles calculations, we find evidence of d-type magnetic impurities in our sample, known to cause impedance in proximal superconductors. This work identifies the structural and chemical composition of the oxide layer grown on Nb superconductors, and shows that soft X-ray absorption can fingerprint magnetic impurities in these superconducting systems.