Motivated by the recent synthesis of Ba$_2$CuO$_{3+delta}$ (BCO), a high temperature superconducting cuprate with putative $d_{3z^2-r^2}$ ground state symmetry, we investigated its electronic structure by means of Cu $L_3$ x-ray absorption (XAS) and resonant inelastic x-ray scattering (RIXS) at the Cu $L_3$ edge on a polycrystalline sample. We show that the XAS profile of BCO is characterised by two peaks associated to inequivalent Cu sites, and that its RIXS response features a single, sharp peak associated to crystal-field excitations. We argue that these observations are only partially compatible with the previously proposed crystal structure of BCO. Based on our spectroscopic results and on previously published powder diffraction measurements, we propose a crystalline structure characterized by two inequivalent Cu sites located at alternated planes along the $c$ axis: nominally trivalent Cu(1) belonging to very short Cu-O chains, and divalent Cu(2) in the oxygen deficient CuO$_ {1.5}$ planes. We also analyze the low-energy region of the RIXS spectra to estimate the magnitude of the magnetic interactions in BCO and find that in-plane nearest neighbor superexchange exceeds 120~meV, similarly to that of other layered cuprates. Although these results do not support the pure $d_{3z^2-r^2}$ ground state scenario, they hint at a significant departure from the common quasi-2D electronic structure of superconducting cuprates of pure $d_{x^2-y^2}$ symmetry.
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