Decoherence remains a critical obstacle to achieving high-fidelity, scalable superconducting qubits, with the tunnel barrier of Josephson junctions a key source of loss, yet the microscopic structure of this buried layer has remained difficult to probe experimentally. Here, we use resonant X-ray reflectivity to resolve the coordination environments within the AlO${}_x$ barrier of Al/AlO${}_x$/Al Josephson junctions as a function of oxidation conditions. We find that the barrier coordination evolves from more tetrahedral toward octahedral character with increasing oxidation pressure, while the lower metal–oxide interface is comparatively under-coordinated and disordered relative to the upper interface. Comparison with simulated X-ray absorption spectra identifies the dominant coordination motifs within the oxide and at its interfaces, providing depth-resolved structural insight that informs microscopic models of two-level system formation. These results link growth conditions, local coordination environments, and junction electronic properties, providing a materials-level foundation for interpreting how the tunnel barrier influences coherence in superconducting qubits.