We investigated the structure of the tungsten bronze barium neodymium titanates Ba6-3nNd8+2nTi18O54, which are exploited as microwave dielectric ceramics. They form a complex nanostructure, which resembles a nanofilm with stacking layers of similar to 12 angstrom thickness. The synthesized samples of Ba6-3nNd8+2nTi18O54 (n = 0, 0.3, 0.4, 0.5) are characterized by pentagonal and tetragonal columns, where the A cations are distributed in three symmetrically inequivalent sites. Synchrotron X-ray diffraction and electron energy loss spectroscopy allowed for quantitative analysis of the site occupancy, which determines the defect distribution. This is corroborated by density functional theory calculations. Pentagonal columns are dominated by Ba, and tetragonal columns are dominated by Nd, although specific Nd sites exhibit significant concentrations of Ba. The data indicated significant elongation of the Ba columns in the pentagonal positions and of the Nd columns in tetragonal positions involving a zigzag arrangement of atoms along the b lattice direction. We found that the preferred Ba substitution occurs at Nd[3]/[4] followed by Nd[2] and Nd[1]/[5] sites, which is significantly different to that proposed in earlier studies. Our results on the Ba6-3nNd8+2nTi18O54 "perovskite" superstructure and its defect distribution are particularly valuable in those applications where the optimization of material properties of oxides is imperative; these include not only microwave ceramics but also thermoelectric materials, where the nanostructure and the distribution of the dopants will reduce the thermal conductivity.